From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 15 Nov 2012 15:15:04 +0000 (+0000)
Subject: Merge branch 'develop' into menard
X-Git-Tag: Jalview_2_9~265^2~27
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=28787d9646cca5dd77190930f59b7ff32cf995b4;p=jalview.git

Merge branch 'develop' into menard

Conflicts:
	src/MCview/PDBfile.java
	src/jalview/analysis/Rna.java
	src/jalview/analysis/StructureFrequency.java
	src/jalview/appletgui/AlignFrame.java
	src/jalview/datamodel/Sequence.java
	src/jalview/ext/varna/VarnaCommands.java
	src/jalview/gui/AppVarna.java
	src/jalview/gui/AssociatePdbFileWithSeq.java
	src/jalview/gui/PopupMenu.java
	src/jalview/io/FeaturesFile.java
	src/jalview/io/StockholmFile.java
	src/jalview/io/TCoffeeScoreFile.java
	src/jalview/renderer/AnnotationRenderer.java
	src/jalview/schemes/ColourSchemeProperty.java
	src/jalview/schemes/ResidueColourScheme.java
	src/jalview/workers/StrucConsensusThread.java
---

28787d9646cca5dd77190930f59b7ff32cf995b4
diff --cc build.xml
index ba0738e,0f81af7..47a0188
--- a/build.xml
+++ b/build.xml
@@@ -88,9 -88,10 +88,11 @@@
  		<!-- Don't change anything below here unless you know what you are doing! -->
  		<!-- Url path for WebStart in JNLP file -->
  		<property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+ 		<!-- Webstart Image - looked for in resources/images -->
+ 		<property name="WebStartImage" value="JalviewLogo_big.png"/>
  		<!-- J2SE version needed for webstart launch -->
 -		<property name="j2sev" value="1.6+"/>
 +<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 +		<property name="j2sev" value="1.7+"/>
  		<!-- build directory configuration -->
  		<property name="libDir" value="lib" />
  		<property name="resourceDir" value="resources" />
diff --cc src/jalview/analysis/Rna.java
index 800e70a,e386e5c..1583f84
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@@ -69,8 -69,7 +69,7 @@@ public class Rn
          }
          Object temp = stack.pop();
          pairs.addElement(temp);
 -        pairs.addElement(i);
 +        pairs.addElement(i); 
-         //System.out.println(pairs);
        }
  
        i++;
diff --cc src/jalview/analysis/StructureFrequency.java
index 5095ce1,08bb3fd..d57e1c5
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@@ -139,60 -123,41 +140,57 @@@ public class StructureFrequenc
        }
        else
        {
 +    	 
 +    	  
          bpEnd = findPair(rna, i);
 -        if (bpEnd > -1)
 +       
 +        if (bpEnd>-1)
          {
 -          for (j = 0; j < jSize; j++) // foreach row
 +        for (j = 0; j < jSize; j++) // foreach row
 +        {
 +          if (sequences[j] == null)
            {
 -            if (sequences[j] == null)
 +            System.err
 +                    .println("WARNING: Consensus skipping null sequence - possible race condition.");
 +            continue;
 +          }
 +          c = sequences[j].getCharAt(i);
 +          //System.out.println("c="+c);
 +          
 +
 +            // standard representation for gaps in sequence and structure
 +            if (c == '.' || c == ' ')
              {
-               c = '-';
-             }
- 
-             if (c == '-')
-             {
-               values['-']++;
+               System.err
+                       .println("WARNING: Consensus skipping null sequence - possible race condition.");
                continue;
              }
 -            c = sequences[j].getCharAt(i);
 +            cEnd = sequences[j].getCharAt(bpEnd);
 +         
 +         
 +            System.out.println("pairs ="+c+","+cEnd);
 +            if (checkBpType(c, cEnd)==true)
              {
 -
 -              // standard representation for gaps in sequence and structure
 -              if (c == '.' || c == ' ')
 -              {
 -                c = '-';
 -              }
 -
 -              if (c == '-')
 -              {
 -                values['-']++;
 -                continue;
 -              }
 -              cEnd = sequences[j].getCharAt(bpEnd);
 -              if (checkBpType(c, cEnd))
 -              {
 -                values['(']++; // H means it's a helix (structured)
 -              }
 -              pairs[c][cEnd]++;
 -
 +              values['(']++; // H means it's a helix (structured)
                maxResidue = "(";
 +              wooble=true;
 +              System.out.println("It's a pair wc");
 +              
              }
 -          }
 +            if (checkBpType(c, cEnd)==false)
 +            {
 +              wooble =false;
 +              values['[']++; // H means it's a helix (structured)
 +              maxResidue = "[";
 +              System.out.println("It's an pair non canonic");
 +              System.out.println(sequences[j].getRNA());
 +              System.out.println(rnaStruc.getRNAStruc().charAt(i));
 +            }
 +            pairs[c][cEnd]++;  
 +           
 +          
 +        	}
++
          }
          // nonGap++;
        }
diff --cc src/jalview/appletgui/AlignFrame.java
index 01227a6,0f0ba4e..6826266
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@@ -1,3693 -1,3753 +1,3786 @@@
 -/*
 - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
 - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 - * 
 - * This file is part of Jalview.
 - * 
 - * Jalview is free software: you can redistribute it and/or
 - * modify it under the terms of the GNU General Public License 
 - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 - *  
 - * Jalview is distributed in the hope that it will be useful, but 
 - * WITHOUT ANY WARRANTY; without even the implied warranty 
 - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 - * PURPOSE.  See the GNU General Public License for more details.
 - * 
 - * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 - */
 -package jalview.appletgui;
 -
 -import jalview.analysis.AlignmentSorter;
 -import jalview.analysis.Conservation;
 -import jalview.api.SequenceStructureBinding;
 -import jalview.bin.JalviewLite;
 -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;
 -
 -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.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;
 -
 -  public AlignViewport viewport;
 -
 -  int DEFAULT_WIDTH = 700;
 -
 -  int DEFAULT_HEIGHT = 500;
 -
 -  String jalviewServletURL;
 -
 -  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 -          String title, boolean embedded)
 -  {
 -    if (applet != null)
 -    {
 -      jalviewServletURL = applet.getParameter("APPLICATION_URL");
 -    }
 -
 -    try
 -    {
 -      jbInit();
 -    } catch (Exception ex)
 -    {
 -      ex.printStackTrace();
 -    }
 -
 -    viewport = new AlignViewport(al, applet);
 -    alignPanel = new AlignmentPanel(this, viewport);
 -
 -    viewport.updateConservation(alignPanel);
 -    viewport.updateConsensus(alignPanel);
 -
 -    annotationPanelMenuItem.setState(viewport.showAnnotation);
 -    displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 -    followMouseOverFlag.setState(viewport.getFollowHighlight());
 -    showGroupConsensus.setState(viewport.isShowGroupConsensus());
 -    showGroupConservation.setState(viewport.isShowGroupConservation());
 -    showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 -    showSequenceLogo.setState(viewport.isShowSequenceLogo());
 -    normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 -
 -    seqLimits.setState(viewport.showJVSuffix);
 -
 -    if (applet != null)
 -    {
 -      String param = applet.getParameter("sortBy");
 -      if (param != null)
 -      {
 -        if (param.equalsIgnoreCase("Id"))
 -        {
 -          sortIDMenuItem_actionPerformed();
 -        }
 -        else if (param.equalsIgnoreCase("Pairwise Identity"))
 -        {
 -          sortPairwiseMenuItem_actionPerformed();
 -        }
 -        else if (param.equalsIgnoreCase("Length"))
 -        {
 -          sortLengthMenuItem_actionPerformed();
 -        }
 -      }
 -
 -      param = applet.getParameter("wrap");
 -      if (param != null)
 -      {
 -        if (param.equalsIgnoreCase("true"))
 -        {
 -          wrapMenuItem.setState(true);
 -          wrapMenuItem_actionPerformed();
 -        }
 -      }
 -      param = applet.getParameter("centrecolumnlabels");
 -      if (param != null)
 -      {
 -        centreColumnLabelFlag.setState(true);
 -        centreColumnLabelFlag_stateChanged();
 -      }
 -      try
 -      {
 -        param = applet.getParameter("windowWidth");
 -        if (param != null)
 -        {
 -          int width = Integer.parseInt(param);
 -          DEFAULT_WIDTH = width;
 -        }
 -        param = applet.getParameter("windowHeight");
 -        if (param != null)
 -        {
 -          int height = Integer.parseInt(param);
 -          DEFAULT_HEIGHT = height;
 -        }
 -      } catch (Exception ex)
 -      {
 -      }
 -
 -    }
 -    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
 -    this.addKeyListener(this);
 -    alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 -    alignPanel.idPanel.idCanvas.addKeyListener(this);
 -    alignPanel.scalePanel.addKeyListener(this);
 -    alignPanel.annotationPanel.addKeyListener(this);
 -    alignPanel.annotationPanelHolder.addKeyListener(this);
 -    alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 -    alignPanel.alabels.addKeyListener(this);
 -    createAlignFrameWindow(embedded, title);
 -
 -    validate();
 -    alignPanel.adjustAnnotationHeight();
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  public AlignViewport getAlignViewport()
 -  {
 -    return viewport;
 -  }
 -
 -  public SeqCanvas getSeqcanvas()
 -  {
 -    return alignPanel.seqPanel.seqCanvas;
 -  }
 -
 -  /**
 -   * 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
 -   */
 -
 -  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.getAlignment(), alignPanel.seqPanel.seqCanvas
 -                      .getFeatureRenderer().featureColours, featureLinks,
 -                      true, viewport.applet.getDefaultParameter(
 -                              "relaxedidmatch", false));
 -    } catch (Exception ex)
 -    {
 -      ex.printStackTrace();
 -    }
 -
 -    if (featuresFile)
 -    {
 -      if (featureLinks.size() > 0)
 -      {
 -        alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 -      }
 -      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;
 -  }
 -
 -  @Override
 -  public void keyPressed(KeyEvent evt)
 -  {
 -    if (viewport.cursorMode
 -            && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 -                    .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 -                    .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 -            && Character.isDigit(evt.getKeyChar()))
 -      alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 -
 -    switch (evt.getKeyCode())
 -    {
 -    case 27: // escape key
 -      deselectAllSequenceMenuItem_actionPerformed();
 -
 -      alignPanel.alabels.cancelDrag();
 -      break;
 -    case KeyEvent.VK_X:
 -      if (evt.isControlDown() || evt.isMetaDown())
 -      {
 -        cut_actionPerformed();
 -      }
 -      break;
 -    case KeyEvent.VK_C:
 -      if (viewport.cursorMode && !evt.isControlDown())
 -      {
 -        alignPanel.seqPanel.setCursorColumn();
 -      }
 -      if (evt.isControlDown() || evt.isMetaDown())
 -      {
 -        copy_actionPerformed();
 -      }
 -      break;
 -    case KeyEvent.VK_V:
 -      if (evt.isControlDown())
 -      {
 -        paste(evt.isShiftDown());
 -      }
 -      break;
 -    case KeyEvent.VK_A:
 -      if (evt.isControlDown() || evt.isMetaDown())
 -      {
 -        selectAllSequenceMenuItem_actionPerformed();
 -      }
 -      break;
 -    case KeyEvent.VK_DOWN:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.moveCursor(0, 1);
 -      }
 -      else
 -      {
 -        moveSelectedSequences(false);
 -      }
 -      break;
 -
 -    case KeyEvent.VK_UP:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.moveCursor(0, -1);
 -      }
 -      else
 -      {
 -        moveSelectedSequences(true);
 -      }
 -      break;
 -
 -    case KeyEvent.VK_LEFT:
 -      if (evt.isAltDown() || !viewport.cursorMode)
 -        slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 -      else
 -        alignPanel.seqPanel.moveCursor(-1, 0);
 -      break;
 -
 -    case KeyEvent.VK_RIGHT:
 -      if (evt.isAltDown() || !viewport.cursorMode)
 -        slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 -      else
 -        alignPanel.seqPanel.moveCursor(1, 0);
 -      break;
 -
 -    case KeyEvent.VK_SPACE:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 -                || evt.isShiftDown() || evt.isAltDown());
 -      }
 -      break;
 -
 -    case KeyEvent.VK_DELETE:
 -    case KeyEvent.VK_BACK_SPACE:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 -                || evt.isShiftDown() || evt.isAltDown());
 -      }
 -      else
 -      {
 -        cut_actionPerformed();
 -        alignPanel.seqPanel.seqCanvas.repaint();
 -      }
 -      break;
 -
 -    case KeyEvent.VK_S:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.setCursorRow();
 -      }
 -      break;
 -    case KeyEvent.VK_P:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.setCursorPosition();
 -      }
 -      break;
 -
 -    case KeyEvent.VK_ENTER:
 -    case KeyEvent.VK_COMMA:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.setCursorRowAndColumn();
 -      }
 -      break;
 -
 -    case KeyEvent.VK_Q:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 -      }
 -      break;
 -    case KeyEvent.VK_M:
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 -      }
 -      break;
 -
 -    case KeyEvent.VK_F2:
 -      viewport.cursorMode = !viewport.cursorMode;
 -      statusBar.setText("Keyboard editing mode is "
 -              + (viewport.cursorMode ? "on" : "off"));
 -      if (viewport.cursorMode)
 -      {
 -        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 -        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 -      }
 -      break;
 -
 -    case KeyEvent.VK_F:
 -      if (evt.isControlDown())
 -      {
 -        findMenuItem_actionPerformed();
 -      }
 -      break;
 -
 -    case KeyEvent.VK_H:
 -    {
 -      boolean toggleSeqs = !evt.isControlDown();
 -      boolean toggleCols = !evt.isShiftDown();
 -      toggleHiddenRegions(toggleSeqs, toggleCols);
 -      break;
 -    }
 -
 -    case KeyEvent.VK_PAGE_UP:
 -      if (viewport.wrapAlignment)
 -      {
 -        alignPanel.scrollUp(true);
 -      }
 -      else
 -      {
 -        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 -                - viewport.endSeq + viewport.startSeq);
 -      }
 -      break;
 -
 -    case KeyEvent.VK_PAGE_DOWN:
 -      if (viewport.wrapAlignment)
 -      {
 -        alignPanel.scrollUp(false);
 -      }
 -      else
 -      {
 -        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 -                + viewport.endSeq - viewport.startSeq);
 -      }
 -      break;
 -
 -    case KeyEvent.VK_Z:
 -      if (evt.isControlDown())
 -      {
 -        undoMenuItem_actionPerformed();
 -      }
 -      break;
 -
 -    case KeyEvent.VK_Y:
 -      if (evt.isControlDown())
 -      {
 -        redoMenuItem_actionPerformed();
 -      }
 -      break;
 -
 -    case KeyEvent.VK_L:
 -      if (evt.isControlDown())
 -      {
 -        trimAlignment(true);
 -      }
 -      break;
 -
 -    case KeyEvent.VK_R:
 -      if (evt.isControlDown())
 -      {
 -        trimAlignment(false);
 -      }
 -      break;
 -
 -    case KeyEvent.VK_E:
 -      if (evt.isControlDown())
 -      {
 -        if (evt.isShiftDown())
 -        {
 -          this.removeAllGapsMenuItem_actionPerformed();
 -        }
 -        else
 -        {
 -          removeGappedColumnMenuItem_actionPerformed();
 -        }
 -      }
 -      break;
 -    case KeyEvent.VK_I:
 -      if (evt.isControlDown())
 -      {
 -        if (evt.isAltDown())
 -        {
 -          invertColSel_actionPerformed();
 -        }
 -        else
 -        {
 -          invertSequenceMenuItem_actionPerformed();
 -        }
 -      }
 -      break;
 -
 -    case KeyEvent.VK_U:
 -      if (evt.isControlDown())
 -      {
 -        this.deleteGroups_actionPerformed();
 -      }
 -      break;
 -
 -    case KeyEvent.VK_T:
 -      if (evt.isControlDown())
 -      {
 -        newView(null);
 -      }
 -      break;
 -
 -    }
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  /**
 -   * called by key handler and the hide all/show all menu items
 -   * 
 -   * @param toggleSeqs
 -   * @param toggleCols
 -   */
 -  private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 -  {
 -    boolean hide = false;
 -    SequenceGroup sg = viewport.getSelectionGroup();
 -    if (!toggleSeqs && !toggleCols)
 -    {
 -      // Hide everything by the current selection - this is a hack - we do the
 -      // invert and then hide
 -      // first check that there will be visible columns after the invert.
 -      if ((viewport.getColumnSelection() != null
 -              && viewport.getColumnSelection().getSelected() != null && viewport
 -              .getColumnSelection().getSelected().size() > 0)
 -              || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 -                      .getEndRes()))
 -      {
 -        // now invert the sequence set, if required - empty selection implies
 -        // that no hiding is required.
 -        if (sg != null)
 -        {
 -          invertSequenceMenuItem_actionPerformed();
 -          sg = viewport.getSelectionGroup();
 -          toggleSeqs = true;
 -
 -        }
 -        viewport.expandColSelection(sg, true);
 -        // finally invert the column selection and get the new sequence
 -        // selection and indicate it should be hidden.
 -        invertColSel_actionPerformed();
 -        toggleCols = true;
 -      }
 -    }
 -
 -    if (toggleSeqs)
 -    {
 -      if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 -      {
 -        hide = true;
 -        viewport.hideAllSelectedSeqs();
 -      }
 -      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 -              .size() > 0))
 -      {
 -        viewport.showAllHiddenSeqs();
 -      }
 -    }
 -
 -    if (toggleCols)
 -    {
 -      if (viewport.getColumnSelection().getSelected().size() > 0)
 -      {
 -        viewport.hideSelectedColumns();
 -        if (!toggleSeqs)
 -        {
 -          viewport.setSelectionGroup(sg);
 -        }
 -      }
 -      else if (!hide)
 -      {
 -        viewport.showAllHiddenColumns();
 -      }
 -    }
 -  }
 -
 -  @Override
 -  public void keyReleased(KeyEvent evt)
 -  {
 -  }
 -
 -  @Override
 -  public void keyTyped(KeyEvent evt)
 -  {
 -  }
 -
 -  @Override
 -  public void itemStateChanged(ItemEvent evt)
 -  {
 -    if (evt.getSource() == displayNonconservedMenuItem)
 -    {
 -      displayNonconservedMenuItem_actionPerformed();
 -    }
 -    else if (evt.getSource() == colourTextMenuItem)
 -    {
 -      colourTextMenuItem_actionPerformed();
 -    }
 -    else if (evt.getSource() == wrapMenuItem)
 -    {
 -      wrapMenuItem_actionPerformed();
 -    }
 -    else if (evt.getSource() == scaleAbove)
 -    {
 -      viewport.setScaleAboveWrapped(scaleAbove.getState());
 -    }
 -    else if (evt.getSource() == scaleLeft)
 -    {
 -      viewport.setScaleLeftWrapped(scaleLeft.getState());
 -    }
 -    else if (evt.getSource() == scaleRight)
 -    {
 -      viewport.setScaleRightWrapped(scaleRight.getState());
 -    }
 -    else if (evt.getSource() == seqLimits)
 -    {
 -      seqLimits_itemStateChanged();
 -    }
 -    else if (evt.getSource() == viewBoxesMenuItem)
 -    {
 -      viewport.setShowBoxes(viewBoxesMenuItem.getState());
 -    }
 -    else if (evt.getSource() == viewTextMenuItem)
 -    {
 -      viewport.setShowText(viewTextMenuItem.getState());
 -    }
 -    else if (evt.getSource() == renderGapsMenuItem)
 -    {
 -      viewport.setRenderGaps(renderGapsMenuItem.getState());
 -    }
 -    else if (evt.getSource() == annotationPanelMenuItem)
 -    {
 -      viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 -      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 -    }
 -    else if (evt.getSource() == sequenceFeatures)
 -    {
 -      viewport.showSequenceFeatures(sequenceFeatures.getState());
 -      alignPanel.seqPanel.seqCanvas.repaint();
 -    }
 -    else if (evt.getSource() == conservationMenuItem)
 -    {
 -      conservationMenuItem_actionPerformed();
 -    }
 -    else if (evt.getSource() == abovePIDThreshold)
 -    {
 -      abovePIDThreshold_actionPerformed();
 -    }
 -    else if (evt.getSource() == applyToAllGroups)
 -    {
 -      viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 -    }
 -    else if (evt.getSource() == autoCalculate)
 -    {
 -      viewport.autoCalculateConsensus = autoCalculate.getState();
 -    }
 -    else if (evt.getSource() == sortByTree)
 -    {
 -      viewport.sortByTree = sortByTree.getState();
 -    }
 -    else if (evt.getSource() == this.centreColumnLabelFlag)
 -    {
 -      centreColumnLabelFlag_stateChanged();
 -    }
 -    else if (evt.getSource() == this.followMouseOverFlag)
 -    {
 -      mouseOverFlag_stateChanged();
 -    }
 -    else if (evt.getSource() == showGroupConsensus)
 -    {
 -      showGroupConsensus_actionPerformed();
 -    }
 -    else if (evt.getSource() == showGroupConservation)
 -    {
 -      showGroupConservation_actionPerformed();
 -    }
 -    else if (evt.getSource() == showSequenceLogo)
 -    {
 -      showSequenceLogo_actionPerformed();
 -    }
 -    else if (evt.getSource() == normSequenceLogo)
 -    {
 -      normSequenceLogo_actionPerformed();
 -    }
 -    else if (evt.getSource() == showConsensusHistogram)
 -    {
 -      showConsensusHistogram_actionPerformed();
 -    }
 -    else if (evt.getSource() == applyAutoAnnotationSettings)
 -    {
 -      applyAutoAnnotationSettings_actionPerformed();
 -    }
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  private void mouseOverFlag_stateChanged()
 -  {
 -    viewport.followHighlight = followMouseOverFlag.getState();
 -    // TODO: could kick the scrollTo mechanism to reset view for current
 -    // searchresults.
 -  }
 -
 -  private void centreColumnLabelFlag_stateChanged()
 -  {
 -    viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 -    this.alignPanel.annotationPanel.repaint();
 -  }
 -
 -  @Override
 -  public void actionPerformed(ActionEvent evt)
 -  {
 -    Object source = evt.getSource();
 -
 -    if (source == inputText)
 -    {
 -      inputText_actionPerformed();
 -    }
 -    else if (source == loadTree)
 -    {
 -      loadTree_actionPerformed();
 -    }
 -    else if (source == loadApplication)
 -    {
 -      launchFullApplication();
 -    }
 -    else if (source == loadAnnotations)
 -    {
 -      loadAnnotations();
 -    }
 -    else if (source == outputAnnotations)
 -    {
 -      outputAnnotations(true);
 -    }
 -    else if (source == outputFeatures)
 -    {
 -      outputFeatures(true, "Jalview");
 -    }
 -    else if (source == closeMenuItem)
 -    {
 -      closeMenuItem_actionPerformed();
 -    }
 -    else if (source == copy)
 -    {
 -      copy_actionPerformed();
 -    }
 -    else if (source == undoMenuItem)
 -    {
 -      undoMenuItem_actionPerformed();
 -    }
 -    else if (source == redoMenuItem)
 -    {
 -      redoMenuItem_actionPerformed();
 -    }
 -    else if (source == inputText)
 -    {
 -      inputText_actionPerformed();
 -    }
 -    else if (source == closeMenuItem)
 -    {
 -      closeMenuItem_actionPerformed();
 -    }
 -    else if (source == undoMenuItem)
 -    {
 -      undoMenuItem_actionPerformed();
 -    }
 -    else if (source == redoMenuItem)
 -    {
 -      redoMenuItem_actionPerformed();
 -    }
 -    else if (source == copy)
 -    {
 -      copy_actionPerformed();
 -    }
 -    else if (source == pasteNew)
 -    {
 -      pasteNew_actionPerformed();
 -    }
 -    else if (source == pasteThis)
 -    {
 -      pasteThis_actionPerformed();
 -    }
 -    else if (source == cut)
 -    {
 -      cut_actionPerformed();
 -    }
 -    else if (source == delete)
 -    {
 -      delete_actionPerformed();
 -    }
 -    else if (source == grpsFromSelection)
 -    {
 -      makeGrpsFromSelection_actionPerformed();
 -    }
 -    else if (source == deleteGroups)
 -    {
 -      deleteGroups_actionPerformed();
 -    }
 -    else if (source == selectAllSequenceMenuItem)
 -    {
 -      selectAllSequenceMenuItem_actionPerformed();
 -    }
 -    else if (source == deselectAllSequenceMenuItem)
 -    {
 -      deselectAllSequenceMenuItem_actionPerformed();
 -    }
 -    else if (source == invertSequenceMenuItem)
 -    {
 -      invertSequenceMenuItem_actionPerformed();
 -    }
 -    else if (source == invertColSel)
 -    {
 -      viewport.invertColumnSelection();
 -      alignPanel.paintAlignment(true);
 -    }
 -    else if (source == remove2LeftMenuItem)
 -    {
 -      trimAlignment(true);
 -    }
 -    else if (source == remove2RightMenuItem)
 -    {
 -      trimAlignment(false);
 -    }
 -    else if (source == removeGappedColumnMenuItem)
 -    {
 -      removeGappedColumnMenuItem_actionPerformed();
 -    }
 -    else if (source == removeAllGapsMenuItem)
 -    {
 -      removeAllGapsMenuItem_actionPerformed();
 -    }
 -    else if (source == findMenuItem)
 -    {
 -      findMenuItem_actionPerformed();
 -    }
 -    else if (source == font)
 -    {
 -      new FontChooser(alignPanel);
 -    }
 -    else if (source == newView)
 -    {
 -      newView(null);
 -    }
 -    else if (source == showColumns)
 -    {
 -      viewport.showAllHiddenColumns();
 -      alignPanel.paintAlignment(true);
 -    }
 -    else if (source == showSeqs)
 -    {
 -      viewport.showAllHiddenSeqs();
 -      alignPanel.paintAlignment(true);
 -    }
 -    else if (source == hideColumns)
 -    {
 -      viewport.hideSelectedColumns();
 -      alignPanel.paintAlignment(true);
 -    }
 -    else if (source == hideSequences
 -            && viewport.getSelectionGroup() != null)
 -    {
 -      viewport.hideAllSelectedSeqs();
 -      alignPanel.paintAlignment(true);
 -    }
 -    else if (source == hideAllButSelection)
 -    {
 -      toggleHiddenRegions(false, false);
 -      alignPanel.paintAlignment(true);
 -    }
 -    else if (source == hideAllSelection)
 -    {
 -      SequenceGroup sg = viewport.getSelectionGroup();
 -      viewport.expandColSelection(sg, false);
 -      viewport.hideAllSelectedSeqs();
 -      viewport.hideSelectedColumns();
 -      alignPanel.paintAlignment(true);
 -    }
 -    else if (source == showAllHidden)
 -    {
 -      viewport.showAllHiddenColumns();
 -      viewport.showAllHiddenSeqs();
 -      alignPanel.paintAlignment(true);
 -    }
 -    else if (source == showGroupConsensus)
 -    {
 -      showGroupConsensus_actionPerformed();
 -    }
 -    else if (source == showGroupConservation)
 -    {
 -      showGroupConservation_actionPerformed();
 -    }
 -    else if (source == showSequenceLogo)
 -    {
 -      showSequenceLogo_actionPerformed();
 -    }
 -    else if (source == normSequenceLogo)
 -    {
 -      normSequenceLogo_actionPerformed();
 -    }
 -    else if (source == showConsensusHistogram)
 -    {
 -      showConsensusHistogram_actionPerformed();
 -    }
 -    else if (source == applyAutoAnnotationSettings)
 -    {
 -      applyAutoAnnotationSettings_actionPerformed();
 -    }
 -    else if (source == featureSettings)
 -    {
 -      new FeatureSettings(alignPanel);
 -    }
 -    else if (source == alProperties)
 -    {
 -      StringBuffer contents = new jalview.io.AlignmentProperties(
 -              viewport.getAlignment()).formatAsString();
 -      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
 -      cap.setText(contents.toString());
 -      Frame frame = new Frame();
 -      frame.add(cap);
 -      jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
 -              + getTitle(), 400, 250);
 -    }
 -    else if (source == overviewMenuItem)
 -    {
 -      overviewMenuItem_actionPerformed();
 -    }
 -    else if (source == noColourmenuItem)
 -    {
 -      changeColour(null);
 -    }
 -    else if (source == clustalColour)
 -    {
 -      abovePIDThreshold.setState(false);
 -      changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
 -    }
 -    else if (source == zappoColour)
 -    {
 -      changeColour(new ZappoColourScheme());
 -    }
 -    else if (source == taylorColour)
 -    {
 -      changeColour(new TaylorColourScheme());
 -    }
 -    else if (source == hydrophobicityColour)
 -    {
 -      changeColour(new HydrophobicColourScheme());
 -    }
 -    else if (source == helixColour)
 -    {
 -      changeColour(new HelixColourScheme());
 -    }
 -    else if (source == strandColour)
 -    {
 -      changeColour(new StrandColourScheme());
 -    }
 -    else if (source == turnColour)
 -    {
 -      changeColour(new TurnColourScheme());
 -    }
 -    else if (source == buriedColour)
 -    {
 -      changeColour(new BuriedColourScheme());
 -    }
 -    else if (source == nucleotideColour)
 -    {
 -      changeColour(new NucleotideColourScheme());
 -    }
 -    else if (source == purinePyrimidineColour)
 -    {
 -      changeColour(new PurinePyrimidineColourScheme());
 -    }
 -    else if (source == RNAHelixColour)
 -    {
 -      new RNAHelicesColourChooser(viewport, alignPanel);
 -    }
 -    else if (source == modifyPID)
 -    {
 -      modifyPID_actionPerformed();
 -    }
 -    else if (source == modifyConservation)
 -    {
 -      modifyConservation_actionPerformed();
 -    }
 -    else if (source == userDefinedColour)
 -    {
 -      new UserDefinedColours(alignPanel, null);
 -    }
 -    else if (source == PIDColour)
 -    {
 -      changeColour(new PIDColourScheme());
 -    }
 -    else if (source == BLOSUM62Colour)
 -    {
 -      changeColour(new Blosum62ColourScheme());
 -    }
 -    else if (source == tcoffeeColour)
 -    {
 -      changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
 -    }
 -    else if (source == annotationColour)
 -    {
 -      new AnnotationColourChooser(viewport, alignPanel);
 -    }
 -    else if (source == sortPairwiseMenuItem)
 -    {
 -      sortPairwiseMenuItem_actionPerformed();
 -    }
 -    else if (source == sortIDMenuItem)
 -    {
 -      sortIDMenuItem_actionPerformed();
 -    }
 -    else if (source == sortLengthMenuItem)
 -    {
 -      sortLengthMenuItem_actionPerformed();
 -    }
 -    else if (source == sortGroupMenuItem)
 -    {
 -      sortGroupMenuItem_actionPerformed();
 -    }
 -    else if (source == removeRedundancyMenuItem)
 -    {
 -      removeRedundancyMenuItem_actionPerformed();
 -    }
 -    else if (source == pairwiseAlignmentMenuItem)
 -    {
 -      pairwiseAlignmentMenuItem_actionPerformed();
 -    }
 -    else if (source == PCAMenuItem)
 -    {
 -      PCAMenuItem_actionPerformed();
 -    }
 -    else if (source == averageDistanceTreeMenuItem)
 -    {
 -      averageDistanceTreeMenuItem_actionPerformed();
 -    }
 -    else if (source == neighbourTreeMenuItem)
 -    {
 -      neighbourTreeMenuItem_actionPerformed();
 -    }
 -    else if (source == njTreeBlosumMenuItem)
 -    {
 -      njTreeBlosumMenuItem_actionPerformed();
 -    }
 -    else if (source == avDistanceTreeBlosumMenuItem)
 -    {
 -      avTreeBlosumMenuItem_actionPerformed();
 -    }
 -    else if (source == documentation)
 -    {
 -      documentation_actionPerformed();
 -    }
 -    else if (source == about)
 -    {
 -      about_actionPerformed();
 -    }
 -
 -  }
 -
 -  public void inputText_actionPerformed()
 -  {
 -    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
 -    Frame frame = new Frame();
 -    frame.add(cap);
 -    jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
 -  }
 -
 -  protected void outputText_actionPerformed(ActionEvent e)
 -  {
 -    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
 -    Frame frame = new Frame();
 -    frame.add(cap);
 -    jalview.bin.JalviewLite.addFrame(frame,
 -            "Alignment output - " + e.getActionCommand(), 600, 500);
 -    cap.setText(new AppletFormatAdapter().formatSequences(
 -            e.getActionCommand(), viewport.getAlignment(),
 -            viewport.showJVSuffix));
 -  }
 -
 -  public void loadAnnotations()
 -  {
 -    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
 -    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.getAlignment()
 -                    .getAlignmentAnnotation() : null, viewport
 -                    .getAlignment().getGroups(), ((Alignment) viewport
 -                    .getAlignment()).alignmentProperties);
 -
 -    if (displayTextbox)
 -    {
 -      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
 -      Frame frame = new Frame();
 -      frame.add(cap);
 -      jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
 -      cap.setText(annotation);
 -    }
 -
 -    return annotation;
 -  }
 -
 -  private Hashtable getDisplayedFeatureCols()
 -  {
 -    if (alignPanel.getFeatureRenderer() != null
 -            && viewport.featuresDisplayed != null)
 -    {
 -      FeatureRenderer fr = alignPanel.getFeatureRenderer();
 -      Hashtable fcols = new Hashtable();
 -      Enumeration en = viewport.featuresDisplayed.keys();
 -      while (en.hasMoreElements())
 -      {
 -        Object col = en.nextElement();
 -        fcols.put(col, fr.featureColours.get(col));
 -      }
 -      return fcols;
 -    }
 -    return null;
 -  }
 -
 -  public String outputFeatures(boolean displayTextbox, String format)
 -  {
 -    String features;
 -    if (format.equalsIgnoreCase("Jalview"))
 -    {
 -      features = new FeaturesFile().printJalviewFormat(viewport
 -              .getAlignment().getSequencesArray(),
 -              getDisplayedFeatureCols());
 -    }
 -    else
 -    {
 -      features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
 -              .getSequencesArray(), getDisplayedFeatureCols());
 -    }
 -
 -    if (displayTextbox)
 -    {
 -      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;
 -  }
 -
 -  void launchFullApplication()
 -  {
 -    StringBuffer url = new StringBuffer(jalviewServletURL);
 -
 -    url.append("?open="
 -            + appendProtocol(viewport.applet.getParameter("file")));
 -
 -    if (viewport.applet.getParameter("features") != null)
 -    {
 -      url.append("&features=");
 -      url.append(appendProtocol(viewport.applet.getParameter("features")));
 -    }
 -
 -    if (viewport.applet.getParameter("annotations") != null)
 -    {
 -      url.append("&annotations=");
 -      url.append(appendProtocol(viewport.applet.getParameter("annotations")));
 -    }
 -
 -    if (viewport.applet.getParameter("jnetfile") != null)
 -    {
 -      url.append("&annotations=");
 -      url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
 -    }
 -
 -    if (viewport.applet.getParameter("defaultColour") != null)
 -    {
 -      url.append("&colour="
 -              + removeWhiteSpace(viewport.applet
 -                      .getParameter("defaultColour")));
 -    }
 -
 -    if (viewport.applet.getParameter("userDefinedColour") != null)
 -    {
 -      url.append("&colour="
 -              + removeWhiteSpace(viewport.applet
 -                      .getParameter("userDefinedColour")));
 -    }
 -    if (viewport.applet.getParameter("tree") != null)
 -    {
 -      url.append("&tree="
 -              + appendProtocol(viewport.applet.getParameter("tree")));
 -    }
 -    if (viewport.applet.getParameter("treeFile") != null)
 -    {
 -      url.append("&tree="
 -              + appendProtocol(viewport.applet.getParameter("treeFile")));
 -    }
 -
 -    showURL(url.toString(), "FULL_APP");
 -  }
 -
 -  String removeWhiteSpace(String colour)
 -  {
 -    StringBuffer sb = new StringBuffer();
 -    for (int i = 0; i < colour.length(); i++)
 -    {
 -      if (Character.isWhitespace(colour.charAt(i)))
 -      {
 -        sb.append("%20");
 -      }
 -      else
 -      {
 -        sb.append(colour.charAt(i));
 -      }
 -    }
 -
 -    return sb.toString();
 -  }
 -
 -  String appendProtocol(String url)
 -  {
 -    try
 -    {
 -      new URL(url);
 -      url = URLEncoder.encode(url);
 -    }
 -    /*
 -     * When we finally deprecate 1.1 compatibility, we can start to use
 -     * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
 -     * (UnsupportedEncodingException ex) { System.err.println("WARNING -
 -     * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
 -     * ex.printStackTrace(); }
 -     */
 -    catch (java.net.MalformedURLException ex)
 -    {
 -      url = viewport.applet.getCodeBase() + url;
 -    }
 -    return url;
 -  }
 -
 -  public void closeMenuItem_actionPerformed()
 -  {
 -    PaintRefresher.RemoveComponent(alignPanel);
 -    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();
 -  }
 -
 -  /**
 -   * TODO: JAL-1104
 -   */
 -  void updateEditMenuBar()
 -  {
 -
 -    if (viewport.historyList.size() > 0)
 -    {
 -      undoMenuItem.setEnabled(true);
 -      CommandI command = (CommandI) viewport.historyList.peek();
 -      undoMenuItem.setLabel("Undo " + command.getDescription());
 -    }
 -    else
 -    {
 -      undoMenuItem.setEnabled(false);
 -      undoMenuItem.setLabel("Undo");
 -    }
 -
 -    if (viewport.redoList.size() > 0)
 -    {
 -      redoMenuItem.setEnabled(true);
 -
 -      CommandI command = (CommandI) viewport.redoList.peek();
 -      redoMenuItem.setLabel("Redo " + command.getDescription());
 -    }
 -    else
 -    {
 -      redoMenuItem.setEnabled(false);
 -      redoMenuItem.setLabel("Redo");
 -    }
 -  }
 -
 -  /**
 -   * TODO: JAL-1104
 -   */
 -  public void addHistoryItem(CommandI command)
 -  {
 -    if (command.getSize() > 0)
 -    {
 -      viewport.historyList.push(command);
 -      viewport.redoList.removeAllElements();
 -      updateEditMenuBar();
 -      viewport.updateHiddenColumns();
 -    }
 -  }
 -
 -  /**
 -   * TODO: JAL-1104 DOCUMENT ME!
 -   * 
 -   * @param e
 -   *          DOCUMENT ME!
 -   */
 -  protected void undoMenuItem_actionPerformed()
 -  {
 -    if (viewport.historyList.size() < 1)
 -    {
 -      return;
 -    }
 -
 -    CommandI command = (CommandI) viewport.historyList.pop();
 -    viewport.redoList.push(command);
 -    command.undoCommand(null);
 -
 -    AlignViewport originalSource = getOriginatingSource(command);
 -    // 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
 -            .getAlignment().getSequences());
 -  }
 -
 -  /**
 -   * TODO: JAL-1104 DOCUMENT ME!
 -   * 
 -   * @param e
 -   *          DOCUMENT ME!
 -   */
 -  protected void redoMenuItem_actionPerformed()
 -  {
 -    if (viewport.redoList.size() < 1)
 -    {
 -      return;
 -    }
 -
 -    CommandI command = (CommandI) viewport.redoList.pop();
 -    viewport.historyList.push(command);
 -    command.doCommand(null);
 -
 -    AlignViewport originalSource = getOriginatingSource(command);
 -    // 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
 -            .getAlignment().getSequences());
 -  }
 -
 -  AlignViewport getOriginatingSource(CommandI command)
 -  {
 -    AlignViewport originalSource = null;
 -    // For sequence removal and addition, we need to fire
 -    // the property change event FROM the viewport where the
 -    // original alignment was altered
 -    AlignmentI al = null;
 -    if (command instanceof EditCommand)
 -    {
 -      EditCommand editCommand = (EditCommand) command;
 -      al = editCommand.getAlignment();
 -      Vector comps = (Vector) PaintRefresher.components.get(viewport
 -              .getSequenceSetId());
 -      for (int i = 0; i < comps.size(); i++)
 -      {
 -        if (comps.elementAt(i) instanceof AlignmentPanel)
 -        {
 -          if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
 -          {
 -            originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
 -            break;
 -          }
 -        }
 -      }
 -    }
 -
 -    if (originalSource == null)
 -    {
 -      // The original view is closed, we must validate
 -      // the current view against the closed view first
 -      if (al != null)
 -      {
 -        PaintRefresher.validateSequences(al, viewport.getAlignment());
 -      }
 -
 -      originalSource = viewport;
 -    }
 -
 -    return originalSource;
 -  }
 -
 -  public void moveSelectedSequences(boolean up)
 -  {
 -    SequenceGroup sg = viewport.getSelectionGroup();
 -    if (sg == null)
 -    {
 -      return;
 -    }
 -    viewport.getAlignment().moveSelectedSequencesByOne(sg,
 -            up ? null : viewport.getHiddenRepSequences(), up);
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  synchronized void slideSequences(boolean right, int size)
 -  {
 -    List<SequenceI> sg = new Vector<SequenceI>();
 -    if (viewport.cursorMode)
 -    {
 -      sg.add(viewport.getAlignment().getSequenceAt(
 -              alignPanel.seqPanel.seqCanvas.cursorY));
 -    }
 -    else if (viewport.getSelectionGroup() != null
 -            && viewport.getSelectionGroup().getSize() != viewport
 -                    .getAlignment().getHeight())
 -    {
 -      sg = viewport.getSelectionGroup().getSequences(
 -              viewport.getHiddenRepSequences());
 -    }
 -
 -    if (sg.size() < 1)
 -    {
 -      return;
 -    }
 -
 -    Vector<SequenceI> invertGroup = new Vector();
 -
 -    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
 -    {
 -      if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
 -        invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
 -    }
 -
 -    SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
 -
 -    SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
 -            .size()]);
 -    for (int i = 0; i < invertGroup.size(); i++)
 -      seqs2[i] = invertGroup.elementAt(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);
 -      else
 -        groupAdjustment = size;
 -    }
 -    else if (!ssc.getGapsInsertedBegin() && !right)
 -    {
 -      if (viewport.cursorMode)
 -        alignPanel.seqPanel.moveCursor(-size, 0);
 -      else
 -        groupAdjustment = -size;
 -    }
 -
 -    if (groupAdjustment != 0)
 -    {
 -      viewport.getSelectionGroup().setStartRes(
 -              viewport.getSelectionGroup().getStartRes() + groupAdjustment);
 -      viewport.getSelectionGroup().setEndRes(
 -              viewport.getSelectionGroup().getEndRes() + groupAdjustment);
 -    }
 -
 -    boolean appendHistoryItem = false;
 -    if (viewport.historyList != null && viewport.historyList.size() > 0
 -            && viewport.historyList.peek() instanceof SlideSequencesCommand)
 -    {
 -      appendHistoryItem = ssc
 -              .appendSlideCommand((SlideSequencesCommand) viewport.historyList
 -                      .peek());
 -    }
 -
 -    if (!appendHistoryItem)
 -      addHistoryItem(ssc);
 -
 -    repaint();
 -  }
 -
 -  static StringBuffer copiedSequences;
 -
 -  static Vector copiedHiddenColumns;
 -
 -  protected void copy_actionPerformed()
 -  {
 -    if (viewport.getSelectionGroup() == null)
 -    {
 -      return;
 -    }
 -
 -    SequenceGroup sg = viewport.getSelectionGroup();
 -    copiedSequences = new StringBuffer();
 -    Hashtable orderedSeqs = new Hashtable();
 -    for (int i = 0; i < sg.getSize(); i++)
 -    {
 -      SequenceI seq = sg.getSequenceAt(i);
 -      int index = viewport.getAlignment().findIndex(seq);
 -      orderedSeqs.put(index + "", seq);
 -    }
 -
 -    int index = 0, startRes, endRes;
 -    char ch;
 -
 -    if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
 -    {
 -      copiedHiddenColumns = new Vector();
 -      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
 -      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
 -              .size(); i++)
 -      {
 -        int[] region = (int[]) viewport.getColumnSelection()
 -                .getHiddenColumns().elementAt(i);
 -
 -        copiedHiddenColumns.addElement(new int[]
 -        { region[0] - hiddenOffset, region[1] - hiddenOffset });
 -      }
 -    }
 -    else
 -    {
 -      copiedHiddenColumns = null;
 -    }
 -
 -    for (int i = 0; i < sg.getSize(); i++)
 -    {
 -      SequenceI seq = null;
 -
 -      while (seq == null)
 -      {
 -        if (orderedSeqs.containsKey(index + ""))
 -        {
 -          seq = (SequenceI) orderedSeqs.get(index + "");
 -          index++;
 -
 -          break;
 -        }
 -        else
 -        {
 -          index++;
 -        }
 -      }
 -
 -      // FIND START RES
 -      // Returns residue following index if gap
 -      startRes = seq.findPosition(sg.getStartRes());
 -
 -      // FIND END RES
 -      // Need to find the residue preceeding index if gap
 -      endRes = 0;
 -
 -      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
 -      {
 -        ch = seq.getCharAt(j);
 -        if (!jalview.util.Comparison.isGap((ch)))
 -        {
 -          endRes++;
 -        }
 -      }
 -
 -      if (endRes > 0)
 -      {
 -        endRes += seq.getStart() - 1;
 -      }
 -
 -      copiedSequences.append(seq.getName()
 -              + "\t"
 -              + startRes
 -              + "\t"
 -              + endRes
 -              + "\t"
 -              + seq.getSequenceAsString(sg.getStartRes(),
 -                      sg.getEndRes() + 1) + "\n");
 -    }
 -
 -  }
 -
 -  protected void pasteNew_actionPerformed()
 -  {
 -    paste(true);
 -  }
 -
 -  protected void pasteThis_actionPerformed()
 -  {
 -    paste(false);
 -  }
 -
 -  void paste(boolean newAlignment)
 -  {
 -    try
 -    {
 -
 -      if (copiedSequences == null)
 -      {
 -        return;
 -      }
 -
 -      StringTokenizer st = new StringTokenizer(copiedSequences.toString());
 -      Vector seqs = new Vector();
 -      while (st.hasMoreElements())
 -      {
 -        String name = st.nextToken();
 -        int start = Integer.parseInt(st.nextToken());
 -        int end = Integer.parseInt(st.nextToken());
 -        seqs.addElement(new Sequence(name, st.nextToken(), start, end));
 -      }
 -      SequenceI[] newSeqs = new SequenceI[seqs.size()];
 -      for (int i = 0; i < seqs.size(); i++)
 -      {
 -        newSeqs[i] = (SequenceI) seqs.elementAt(i);
 -      }
 -
 -      if (newAlignment)
 -      {
 -        String newtitle = new String("Copied sequences");
 -        if (getTitle().startsWith("Copied sequences"))
 -        {
 -          newtitle = getTitle();
 -        }
 -        else
 -        {
 -          newtitle = newtitle.concat("- from " + getTitle());
 -        }
 -        AlignFrame af = new AlignFrame(new Alignment(newSeqs),
 -                viewport.applet, newtitle, false);
 -        if (copiedHiddenColumns != null)
 -        {
 -          for (int i = 0; i < copiedHiddenColumns.size(); i++)
 -          {
 -            int[] region = (int[]) copiedHiddenColumns.elementAt(i);
 -            af.viewport.hideColumns(region[0], region[1]);
 -          }
 -        }
 -
 -        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
 -                DEFAULT_HEIGHT);
 -      }
 -      else
 -      {
 -        addSequences(newSeqs);
 -      }
 -
 -    } catch (Exception ex)
 -    {
 -    } // could be anything being pasted in here
 -
 -  }
 -
 -  void addSequences(SequenceI[] seqs)
 -  {
 -    for (int i = 0; i < seqs.length; i++)
 -    {
 -      viewport.getAlignment().addSequence(seqs[i]);
 -    }
 -
 -    // !newAlignment
 -    addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
 -            seqs, 0, viewport.getAlignment().getWidth(),
 -            viewport.getAlignment()));
 -
 -    viewport.setEndSeq(viewport.getAlignment().getHeight());
 -    viewport.getAlignment().getWidth();
 -    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
 -            .getSequences());
 -
 -  }
 -
 -  protected void cut_actionPerformed()
 -  {
 -    copy_actionPerformed();
 -    delete_actionPerformed();
 -  }
 -
 -  protected void delete_actionPerformed()
 -  {
 -
 -    SequenceGroup sg = viewport.getSelectionGroup();
 -    if (sg == null)
 -    {
 -      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 (sg.getSize() == viewport.getAlignment().getHeight())
 -    {
 -      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);
 -    }
 -
 -    /*
 -     * //ADD HISTORY ITEM
 -     */
 -    addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
 -            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
 -            viewport.getAlignment()));
 -
 -    viewport.setSelectionGroup(null);
 -    viewport.getAlignment().deleteGroup(sg);
 -
 -    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
 -            .getSequences());
 -
 -    if (viewport.getAlignment().getHeight() < 1)
 -    {
 -      this.setVisible(false);
 -    }
 -    viewport.sendSelection();
 -  }
 -
 -  /**
 -   * group consensus toggled
 -   * 
 -   */
 -  protected void showGroupConsensus_actionPerformed()
 -  {
 -    viewport.setShowGroupConsensus(showGroupConsensus.getState());
 -    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 -
 -  }
 -
 -  /**
 -   * group conservation toggled.
 -   */
 -  protected void showGroupConservation_actionPerformed()
 -  {
 -    viewport.setShowGroupConservation(showGroupConservation.getState());
 -    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 -  }
 -
 -  /*
 -   * (non-Javadoc)
 -   * 
 -   * @see
 -   * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
 -   * .event.ActionEvent)
 -   */
 -  protected void showConsensusHistogram_actionPerformed()
 -  {
 -    viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
 -    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 -  }
 -
 -  /*
 -   * (non-Javadoc)
 -   * 
 -   * @see
 -   * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
 -   * .event.ActionEvent)
 -   */
 -  protected void showSequenceLogo_actionPerformed()
 -  {
 -    viewport.setShowSequenceLogo(showSequenceLogo.getState());
 -    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 -  }
 -
 -  protected void normSequenceLogo_actionPerformed()
 -  {
 -    showSequenceLogo.setState(true);
 -    viewport.setShowSequenceLogo(true);
 -    viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
 -    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 -  }
 -
 -  protected void applyAutoAnnotationSettings_actionPerformed()
 -  {
 -    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 -  }
 -
 -  protected void makeGrpsFromSelection_actionPerformed()
 -  {
 -    if (viewport.getSelectionGroup() != null)
 -    {
 -      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
 -              viewport.getSequenceSelection(),
 -              viewport.getAlignmentView(true).getSequenceStrings(
 -                      viewport.getGapCharacter()), viewport.getAlignment()
 -                      .getGroups());
 -      viewport.getAlignment().deleteAllGroups();
 -      viewport.sequenceColours = null;
 -      viewport.setSelectionGroup(null);
 -      // set view properties for each group
 -      for (int g = 0; g < gps.length; g++)
 -      {
 -        // gps[g].setShowunconserved(viewport.getShowUnconserved());
 -        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
 -        viewport.getAlignment().addGroup(gps[g]);
 -        Color col = new Color((int) (Math.random() * 255),
 -                (int) (Math.random() * 255), (int) (Math.random() * 255));
 -        col = col.brighter();
 -        for (SequenceI sq : gps[g].getSequences(null))
 -          viewport.setSequenceColour(sq, col);
 -      }
 -      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
 -      alignPanel.updateAnnotation();
 -      alignPanel.paintAlignment(true);
 -    }
 -  }
 -
 -  protected void deleteGroups_actionPerformed()
 -  {
 -    viewport.getAlignment().deleteAllGroups();
 -    viewport.sequenceColours = null;
 -    viewport.setSelectionGroup(null);
 -
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  public void selectAllSequenceMenuItem_actionPerformed()
 -  {
 -    SequenceGroup sg = new SequenceGroup();
 -    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 -    {
 -      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
 -    }
 -    sg.setEndRes(viewport.getAlignment().getWidth() - 1);
 -    viewport.setSelectionGroup(sg);
 -    alignPanel.paintAlignment(true);
 -    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
 -    viewport.sendSelection();
 -  }
 -
 -  public void deselectAllSequenceMenuItem_actionPerformed()
 -  {
 -    if (viewport.cursorMode)
 -    {
 -      alignPanel.seqPanel.keyboardNo1 = null;
 -      alignPanel.seqPanel.keyboardNo2 = null;
 -    }
 -    viewport.setSelectionGroup(null);
 -    viewport.getColumnSelection().clear();
 -    viewport.setSelectionGroup(null);
 -    alignPanel.idPanel.idCanvas.searchResults = null;
 -    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
 -    alignPanel.paintAlignment(true);
 -    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
 -    viewport.sendSelection();
 -  }
 -
 -  public void invertSequenceMenuItem_actionPerformed()
 -  {
 -    SequenceGroup sg = viewport.getSelectionGroup();
 -    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 -    {
 -      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
 -    }
 -
 -    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
 -    viewport.sendSelection();
 -  }
 -
 -  public void invertColSel_actionPerformed()
 -  {
 -    viewport.invertColumnSelection();
 -    alignPanel.paintAlignment(true);
 -    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
 -    viewport.sendSelection();
 -  }
 -
 -  void trimAlignment(boolean trimLeft)
 -  {
 -    ColumnSelection colSel = viewport.getColumnSelection();
 -    int column;
 -
 -    if (colSel.size() > 0)
 -    {
 -      if (trimLeft)
 -      {
 -        column = colSel.getMin();
 -      }
 -      else
 -      {
 -        column = colSel.getMax();
 -      }
 -
 -      SequenceI[] seqs;
 -      if (viewport.getSelectionGroup() != null)
 -      {
 -        seqs = viewport.getSelectionGroup().getSequencesAsArray(
 -                viewport.getHiddenRepSequences());
 -      }
 -      else
 -      {
 -        seqs = viewport.getAlignment().getSequencesArray();
 -      }
 -
 -      TrimRegionCommand trimRegion;
 -      if (trimLeft)
 -      {
 -        trimRegion = new TrimRegionCommand("Remove Left",
 -                TrimRegionCommand.TRIM_LEFT, seqs, column,
 -                viewport.getAlignment(), viewport.getColumnSelection(),
 -                viewport.getSelectionGroup());
 -        viewport.setStartRes(0);
 -      }
 -      else
 -      {
 -        trimRegion = new TrimRegionCommand("Remove Right",
 -                TrimRegionCommand.TRIM_RIGHT, seqs, column,
 -                viewport.getAlignment(), viewport.getColumnSelection(),
 -                viewport.getSelectionGroup());
 -      }
 -
 -      statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
 -
 -      addHistoryItem(trimRegion);
 -
 -      for (SequenceGroup sg : viewport.getAlignment().getGroups())
 -      {
 -        if ((trimLeft && !sg.adjustForRemoveLeft(column))
 -                || (!trimLeft && !sg.adjustForRemoveRight(column)))
 -        {
 -          viewport.getAlignment().deleteGroup(sg);
 -        }
 -      }
 -
 -      viewport.firePropertyChange("alignment", null, viewport
 -              .getAlignment().getSequences());
 -    }
 -  }
 -
 -  public void removeGappedColumnMenuItem_actionPerformed()
 -  {
 -    int start = 0, end = viewport.getAlignment().getWidth() - 1;
 -
 -    SequenceI[] seqs;
 -    if (viewport.getSelectionGroup() != null)
 -    {
 -      seqs = viewport.getSelectionGroup().getSequencesAsArray(
 -              viewport.getHiddenRepSequences());
 -      start = viewport.getSelectionGroup().getStartRes();
 -      end = viewport.getSelectionGroup().getEndRes();
 -    }
 -    else
 -    {
 -      seqs = viewport.getAlignment().getSequencesArray();
 -    }
 -
 -    RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
 -            "Remove Gapped Columns", seqs, start, end,
 -            viewport.getAlignment());
 -
 -    addHistoryItem(removeGapCols);
 -
 -    statusBar.setText("Removed " + removeGapCols.getSize()
 -            + " empty columns.");
 -
 -    // This is to maintain viewport position on first residue
 -    // of first sequence
 -    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
 -    int startRes = seq.findPosition(viewport.startRes);
 -    // ShiftList shifts;
 -    // viewport.getAlignment().removeGaps(shifts=new ShiftList());
 -    // edit.alColumnChanges=shifts.getInverse();
 -    // if (viewport.hasHiddenColumns)
 -    // viewport.getColumnSelection().compensateForEdits(shifts);
 -    viewport.setStartRes(seq.findIndex(startRes) - 1);
 -    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
 -            .getSequences());
 -
 -  }
 -
 -  public void removeAllGapsMenuItem_actionPerformed()
 -  {
 -    int start = 0, end = viewport.getAlignment().getWidth() - 1;
 -
 -    SequenceI[] seqs;
 -    if (viewport.getSelectionGroup() != null)
 -    {
 -      seqs = viewport.getSelectionGroup().getSequencesAsArray(
 -              viewport.getHiddenRepSequences());
 -      start = viewport.getSelectionGroup().getStartRes();
 -      end = viewport.getSelectionGroup().getEndRes();
 -    }
 -    else
 -    {
 -      seqs = viewport.getAlignment().getSequencesArray();
 -    }
 -
 -    // This is to maintain viewport position on first residue
 -    // of first sequence
 -    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
 -    int startRes = seq.findPosition(viewport.startRes);
 -
 -    addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
 -            viewport.getAlignment()));
 -
 -    viewport.setStartRes(seq.findIndex(startRes) - 1);
 -
 -    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
 -            .getSequences());
 -
 -  }
 -
 -  public void findMenuItem_actionPerformed()
 -  {
 -    new Finder(alignPanel);
 -  }
 -
 -  /**
 -   * create a new view derived from the current view
 -   * 
 -   * @param viewtitle
 -   * @return frame for the new view
 -   */
 -  public AlignFrame newView(String viewtitle)
 -  {
 -    AlignmentI newal;
 -    if (viewport.hasHiddenRows())
 -    {
 -      newal = new Alignment(viewport.getAlignment().getHiddenSequences()
 -              .getFullAlignment().getSequencesArray());
 -    }
 -    else
 -    {
 -      newal = new Alignment(viewport.getAlignment().getSequencesArray());
 -    }
 -
 -    if (viewport.getAlignment().getAlignmentAnnotation() != null)
 -    {
 -      for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
 -      {
 -        if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
 -        {
 -          newal.addAnnotation(viewport.getAlignment()
 -                  .getAlignmentAnnotation()[i]);
 -        }
 -      }
 -    }
 -
 -    AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
 -
 -    newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
 -    PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
 -    PaintRefresher.Register(newaf.alignPanel,
 -            newaf.alignPanel.av.getSequenceSetId());
 -
 -    PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
 -            newaf.alignPanel.av.getSequenceSetId());
 -    PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
 -            newaf.alignPanel.av.getSequenceSetId());
 -
 -    Vector comps = (Vector) PaintRefresher.components.get(viewport
 -            .getSequenceSetId());
 -    int viewSize = -1;
 -    for (int i = 0; i < comps.size(); i++)
 -    {
 -      if (comps.elementAt(i) instanceof AlignmentPanel)
 -      {
 -        viewSize++;
 -      }
 -    }
 -
 -    String title = new String(this.getTitle());
 -    if (viewtitle != null)
 -    {
 -      title = viewtitle + " ( " + title + ")";
 -    }
 -    else
 -    {
 -      if (title.indexOf("(View") > -1)
 -      {
 -        title = title.substring(0, title.indexOf("(View"));
 -      }
 -      title += "(View " + viewSize + ")";
 -    }
 -
 -    newaf.setTitle(title.toString());
 -
 -    newaf.viewport.historyList = viewport.historyList;
 -    newaf.viewport.redoList = viewport.redoList;
 -    return newaf;
 -  }
 -
 -  /**
 -   * 
 -   * @return list of feature groups on the view
 -   */
 -  public String[] getFeatureGroups()
 -  {
 -    FeatureRenderer fr = null;
 -    if (alignPanel != null
 -            && (fr = alignPanel.getFeatureRenderer()) != null)
 -    {
 -      return fr.getGroups();
 -    }
 -    return null;
 -  }
 -
 -  /**
 -   * get sequence feature groups that are hidden or shown
 -   * 
 -   * @param visible
 -   *          true is visible
 -   * @return list
 -   */
 -  public String[] getFeatureGroupsOfState(boolean visible)
 -  {
 -    FeatureRenderer fr = null;
 -    if (alignPanel != null
 -            && (fr = alignPanel.getFeatureRenderer()) != null)
 -    {
 -      return fr.getGroups(visible);
 -    }
 -    return null;
 -  }
 -
 -  /**
 -   * Change the display state for the given feature groups
 -   * 
 -   * @param groups
 -   *          list of group strings
 -   * @param state
 -   *          visible or invisible
 -   */
 -  public void setFeatureGroupState(String[] groups, boolean state)
 -  {
 -    FeatureRenderer fr = null;
 -    this.sequenceFeatures.setState(true);
 -    viewport.showSequenceFeatures(true);
 -    if (alignPanel != null
 -            && (fr = alignPanel.getFeatureRenderer()) != null)
 -    {
 -      fr.setGroupState(groups, state);
 -      alignPanel.seqPanel.seqCanvas.repaint();
 -      if (alignPanel.overviewPanel != null)
 -      {
 -        alignPanel.overviewPanel.updateOverviewImage();
 -      }
 -    }
 -  }
 -
 -  public void seqLimits_itemStateChanged()
 -  {
 -    viewport.setShowJVSuffix(seqLimits.getState());
 -    alignPanel.fontChanged();
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  protected void colourTextMenuItem_actionPerformed()
 -  {
 -    viewport.setColourText(colourTextMenuItem.getState());
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  protected void displayNonconservedMenuItem_actionPerformed()
 -  {
 -    viewport.setShowunconserved(displayNonconservedMenuItem.getState());
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  protected void wrapMenuItem_actionPerformed()
 -  {
 -    viewport.setWrapAlignment(wrapMenuItem.getState());
 -    alignPanel.setWrapAlignment(wrapMenuItem.getState());
 -    scaleAbove.setEnabled(wrapMenuItem.getState());
 -    scaleLeft.setEnabled(wrapMenuItem.getState());
 -    scaleRight.setEnabled(wrapMenuItem.getState());
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  public void overviewMenuItem_actionPerformed()
 -  {
 -    if (alignPanel.overviewPanel != null)
 -    {
 -      return;
 -    }
 -
 -    Frame frame = new Frame();
 -    OverviewPanel overview = new OverviewPanel(alignPanel);
 -    frame.add(overview);
 -    // +50 must allow for applet frame window
 -    jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
 -            overview.getPreferredSize().width,
 -            overview.getPreferredSize().height + 50);
 -
 -    frame.pack();
 -    final AlignmentPanel ap = alignPanel;
 -    frame.addWindowListener(new WindowAdapter()
 -    {
 -      @Override
 -      public void windowClosing(WindowEvent e)
 -      {
 -        if (ap != null)
 -        {
 -          ap.setOverviewPanel(null);
 -        }
 -      };
 -    });
 -
 -    alignPanel.setOverviewPanel(overview);
 -
 -  }
 -
 -  void changeColour(ColourSchemeI cs)
 -  {
 -    int threshold = 0;
 -
 -    if (cs != null)
 -    {
 -      if (viewport.getAbovePIDThreshold())
 -      {
 -        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
 -                "Background");
 -
 -        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 -
 -        viewport.setGlobalColourScheme(cs);
 -      }
 -      else
 -      {
 -        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
 -      }
 -
 -      if (viewport.getConservationSelected())
 -      {
 -
 -        Alignment al = (Alignment) viewport.getAlignment();
 -        Conservation c = new Conservation("All",
 -                ResidueProperties.propHash, 3, al.getSequences(), 0,
 -                al.getWidth() - 1);
 -
 -        c.calculate();
 -        c.verdict(false, viewport.getConsPercGaps());
 -
 -        cs.setConservation(c);
 -
 -        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
 -                cs, "Background"));
 -
 -      }
 -      else
 -      {
 -        cs.setConservation(null);
 -      }
 -
 -      cs.setConsensus(viewport.getSequenceConsensusHash());
 -
 -    }
 -    viewport.setGlobalColourScheme(cs);
 -
 -    if (alignPanel.getOverviewPanel() != null)
 -    {
 -      alignPanel.getOverviewPanel().updateOverviewImage();
 -    }
 -
 -    jalview.structure.StructureSelectionManager
 -            .getStructureSelectionManager(viewport.applet)
 -            .sequenceColoursChanged(alignPanel);
 -
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  protected void modifyPID_actionPerformed()
 -  {
 -    if (viewport.getAbovePIDThreshold()
 -            && viewport.getGlobalColourScheme() != null)
 -    {
 -      SliderPanel.setPIDSliderSource(alignPanel,
 -              viewport.getGlobalColourScheme(), "Background");
 -      SliderPanel.showPIDSlider();
 -    }
 -  }
 -
 -  protected void modifyConservation_actionPerformed()
 -  {
 -    if (viewport.getConservationSelected()
 -            && viewport.getGlobalColourScheme() != null)
 -    {
 -      SliderPanel.setConservationSlider(alignPanel,
 -              viewport.getGlobalColourScheme(), "Background");
 -      SliderPanel.showConservationSlider();
 -    }
 -  }
 -
 -  protected void conservationMenuItem_actionPerformed()
 -  {
 -    viewport.setConservationSelected(conservationMenuItem.getState());
 -
 -    viewport.setAbovePIDThreshold(false);
 -    abovePIDThreshold.setState(false);
 -
 -    changeColour(viewport.getGlobalColourScheme());
 -
 -    modifyConservation_actionPerformed();
 -  }
 -
 -  public void abovePIDThreshold_actionPerformed()
 -  {
 -    viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
 -
 -    conservationMenuItem.setState(false);
 -    viewport.setConservationSelected(false);
 -
 -    changeColour(viewport.getGlobalColourScheme());
 -
 -    modifyPID_actionPerformed();
 -  }
 -
 -  public void sortPairwiseMenuItem_actionPerformed()
 -  {
 -    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 -    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
 -            .getAlignment().getSequenceAt(0), null);
 -
 -    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
 -            viewport.getAlignment()));
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  public void sortIDMenuItem_actionPerformed()
 -  {
 -    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 -    AlignmentSorter.sortByID(viewport.getAlignment());
 -    addHistoryItem(new OrderCommand("ID Sort", oldOrder,
 -            viewport.getAlignment()));
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  public void sortLengthMenuItem_actionPerformed()
 -  {
 -    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 -    AlignmentSorter.sortByLength(viewport.getAlignment());
 -    addHistoryItem(new OrderCommand("Length Sort", oldOrder,
 -            viewport.getAlignment()));
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  public void sortGroupMenuItem_actionPerformed()
 -  {
 -    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 -    AlignmentSorter.sortByGroup(viewport.getAlignment());
 -    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
 -            viewport.getAlignment()));
 -    alignPanel.paintAlignment(true);
 -
 -  }
 -
 -  public void removeRedundancyMenuItem_actionPerformed()
 -  {
 -    new RedundancyPanel(alignPanel);
 -  }
 -
 -  public void pairwiseAlignmentMenuItem_actionPerformed()
 -  {
 -    if (viewport.getSelectionGroup() != null
 -            && viewport.getSelectionGroup().getSize() > 1)
 -    {
 -      Frame frame = new Frame();
 -      frame.add(new PairwiseAlignPanel(alignPanel));
 -      jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
 -              500);
 -    }
 -  }
 -
 -  public void PCAMenuItem_actionPerformed()
 -  {
 -    // are the sequences aligned?
 -    if (!viewport.getAlignment().isAligned(false))
 -    {
 -      SequenceI current;
 -      int Width = viewport.getAlignment().getWidth();
 -
 -      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 -      {
 -        current = viewport.getAlignment().getSequenceAt(i);
 -
 -        if (current.getLength() < Width)
 -        {
 -          current.insertCharAt(Width - 1, viewport.getGapCharacter());
 -        }
 -      }
 -      alignPanel.paintAlignment(true);
 -    }
 -
 -    if ((viewport.getSelectionGroup() != null
 -            && viewport.getSelectionGroup().getSize() < 4 && viewport
 -            .getSelectionGroup().getSize() > 0)
 -            || viewport.getAlignment().getHeight() < 4)
 -    {
 -      return;
 -    }
 -
 -    try
 -    {
 -      new PCAPanel(viewport);
 -    } catch (java.lang.OutOfMemoryError ex)
 -    {
 -    }
 -
 -  }
 -
 -  public void averageDistanceTreeMenuItem_actionPerformed()
 -  {
 -    NewTreePanel("AV", "PID", "Average distance tree using PID");
 -  }
 -
 -  public void neighbourTreeMenuItem_actionPerformed()
 -  {
 -    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
 -  }
 -
 -  protected void njTreeBlosumMenuItem_actionPerformed()
 -  {
 -    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
 -  }
 -
 -  protected void avTreeBlosumMenuItem_actionPerformed()
 -  {
 -    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
 -  }
 -
 -  void NewTreePanel(String type, String pwType, String title)
 -  {
 -    // are the sequences aligned?
 -    if (!viewport.getAlignment().isAligned(false))
 -    {
 -      SequenceI current;
 -      int Width = viewport.getAlignment().getWidth();
 -
 -      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 -      {
 -        current = viewport.getAlignment().getSequenceAt(i);
 -
 -        if (current.getLength() < Width)
 -        {
 -          current.insertCharAt(Width - 1, viewport.getGapCharacter());
 -        }
 -      }
 -      alignPanel.paintAlignment(true);
 -
 -    }
 -
 -    if ((viewport.getSelectionGroup() != null && viewport
 -            .getSelectionGroup().getSize() > 1)
 -            || (viewport.getAlignment().getHeight() > 1))
 -    {
 -      final TreePanel tp = new TreePanel(alignPanel, type, pwType);
 -
 -      addTreeMenuItem(tp, title);
 -
 -      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
 -    }
 -  }
 -
 -  void loadTree_actionPerformed()
 -  {
 -    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
 -    cap.setText("Paste your Newick tree file here.");
 -    cap.setTreeImport();
 -    Frame frame = new Frame();
 -    frame.add(cap);
 -    jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
 -  }
 -
 -  public void loadTree(jalview.io.NewickFile tree, String treeFile)
 -  {
 -    TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
 -    jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
 -    addTreeMenuItem(tp, treeFile);
 -  }
 -
 -  /**
 -   * sort the alignment using the given treePanel
 -   * 
 -   * @param treePanel
 -   *          tree used to sort view
 -   * @param title
 -   *          string used for undo event name
 -   */
 -  public void sortByTree(TreePanel treePanel, String title)
 -  {
 -    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 -    AlignmentSorter
 -            .sortByTree(viewport.getAlignment(), treePanel.getTree());
 -    // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
 -    // HistoryItem.SORT));
 -    addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
 -            viewport.getAlignment()));
 -    alignPanel.paintAlignment(true);
 -  }
 -
 -  /**
 -   * Do any automatic reordering of the alignment and add the necessary bits to
 -   * the menu structure for the new tree
 -   * 
 -   * @param treePanel
 -   * @param title
 -   */
 -  protected void addTreeMenuItem(final TreePanel treePanel,
 -          final String title)
 -  {
 -    final MenuItem item = new MenuItem(title);
 -    sortByTreeMenu.add(item);
 -    item.addActionListener(new java.awt.event.ActionListener()
 -    {
 -      @Override
 -      public void actionPerformed(ActionEvent evt)
 -      {
 -        sortByTree(treePanel, title); // treePanel.getTitle());
 -      }
 -    });
 -
 -    treePanel.addWindowListener(new WindowAdapter()
 -    {
 -      @Override
 -      public void windowOpened(WindowEvent e)
 -      {
 -        if (viewport.sortByTree)
 -        {
 -          sortByTree(treePanel, title);
 -        }
 -        super.windowOpened(e);
 -      }
 -
 -      @Override
 -      public void windowClosing(WindowEvent e)
 -      {
 -        sortByTreeMenu.remove(item);
 -      };
 -    });
 -  }
 -
 -  public boolean sortBy(AlignmentOrder alorder, String undoname)
 -  {
 -    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 -    if (viewport.applet.debug)
 -    {
 -      System.err.println("Sorting " + alorder.getOrder().size()
 -              + " in alignment '" + getTitle() + "'");
 -    }
 -    AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
 -    if (undoname != null)
 -    {
 -      addHistoryItem(new OrderCommand(undoname, oldOrder,
 -              viewport.getAlignment()));
 -    }
 -    alignPanel.paintAlignment(true);
 -    return true;
 -  }
 -
 -  protected void documentation_actionPerformed()
 -  {
 -    alignPanel.av.applet.openJalviewHelpUrl();
 -  }
 -
 -  protected void about_actionPerformed()
 -  {
 -
 -    class AboutPanel extends Canvas
 -    {
 -      String version;
 -
 -      String builddate;
 -
 -      public AboutPanel(String version, String builddate)
 -      {
 -        this.version = version;
 -        this.builddate = builddate;
 -      }
 -
 -      @Override
 -      public void paint(Graphics g)
 -      {
 -        g.setColor(Color.white);
 -        g.fillRect(0, 0, getSize().width, getSize().height);
 -        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
 -        FontMetrics fm = g.getFontMetrics();
 -        int fh = fm.getHeight();
 -        int y = 5, x = 7;
 -        g.setColor(Color.black);
 -        // TODO: update this text for each release or centrally store it for
 -        // lite and application
 -        g.setFont(new Font("Helvetica", Font.BOLD, 14));
 -        g.drawString("JalviewLite - Release " + version, x, y += fh);
 -        g.setFont(new Font("Helvetica", Font.BOLD, 12));
 -        g.drawString("Build date: " + builddate, x, y += fh);
 -        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
 -        g.drawString(
 -                "Authors:  Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
 -                x, y += fh * 1.5);
 -        g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
 -        g.drawString(
 -                "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
 -                x, y += fh);
 -        g.drawString(
 -                "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
 -                x, y += fh);
 -        g.drawString("If  you use Jalview, please cite:", x, y += fh + 8);
 -        g.drawString(
 -                "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
 -                x, y += fh);
 -        g.drawString(
 -                "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
 -                x, y += fh);
 -        g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
 -                x, y += fh);
 -      }
 -    }
 -
 -    Frame frame = new Frame();
 -    frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
 -            .getBuildDate()));
 -    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
 -
 -  }
 -
 -  public void showURL(String url, String target)
 -  {
 -    if (viewport.applet == null)
 -    {
 -      System.out.println("Not running as applet - no browser available.");
 -    }
 -    else
 -    {
 -      viewport.applet.showURL(url, target);
 -    }
 -  }
 -
 -  // ////////////////////////////////////////////////////////////////////////////////
 -  // JBuilder Graphics here
 -
 -  MenuBar alignFrameMenuBar = new MenuBar();
 -
 -  Menu fileMenu = new Menu("File");
 -
 -  MenuItem loadApplication = new MenuItem("View in Full Application");
 -
 -  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 ...");
 -
 -  MenuItem closeMenuItem = new MenuItem("Close");
 -
 -  Menu editMenu = new Menu("Edit");
 -
 -  Menu viewMenu = new Menu("View");
 -
 -  Menu colourMenu = new Menu("Colour");
 -
 -  Menu calculateMenu = new Menu("Calculate");
 -
 -  MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
 -
 -  MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
 -
 -  MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
 -
 -  MenuItem remove2LeftMenuItem = new MenuItem();
 -
 -  MenuItem remove2RightMenuItem = new MenuItem();
 -
 -  MenuItem removeGappedColumnMenuItem = new MenuItem();
 -
 -  MenuItem removeAllGapsMenuItem = new MenuItem();
 -
 -  CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
 -
 -  MenuItem sortPairwiseMenuItem = new MenuItem();
 -
 -  MenuItem sortIDMenuItem = new MenuItem();
 -
 -  MenuItem sortLengthMenuItem = new MenuItem();
 -
 -  MenuItem sortGroupMenuItem = new MenuItem();
 -
 -  MenuItem removeRedundancyMenuItem = new MenuItem();
 -
 -  MenuItem pairwiseAlignmentMenuItem = new MenuItem();
 -
 -  MenuItem PCAMenuItem = new MenuItem();
 -
 -  MenuItem averageDistanceTreeMenuItem = new MenuItem();
 -
 -  MenuItem neighbourTreeMenuItem = new MenuItem();
 -
 -  BorderLayout borderLayout1 = new BorderLayout();
 -
 -  public Label statusBar = new Label();
 -
 -  Menu outputTextboxMenu = new Menu();
 -
 -  MenuItem clustalColour = new MenuItem();
 -
 -  MenuItem zappoColour = new MenuItem();
 -
 -  MenuItem taylorColour = new MenuItem();
 -
 -  MenuItem hydrophobicityColour = new MenuItem();
 -
 -  MenuItem helixColour = new MenuItem();
 -
 -  MenuItem strandColour = new MenuItem();
 -
 -  MenuItem turnColour = new MenuItem();
 -
 -  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();
 -
 -  MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
 -
 -  CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
 -
 -  MenuItem alProperties = new MenuItem("Alignment Properties...");
 -
 -  MenuItem overviewMenuItem = new MenuItem();
 -
 -  MenuItem undoMenuItem = new MenuItem();
 -
 -  MenuItem redoMenuItem = new MenuItem();
 -
 -  CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 -
 -  MenuItem noColourmenuItem = new MenuItem();
 -
 -  CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
 -
 -  MenuItem findMenuItem = new MenuItem();
 -
 -  CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
 -
 -  MenuItem nucleotideColour = new MenuItem();
 -
 -  MenuItem deleteGroups = new MenuItem();
 -
 -  MenuItem grpsFromSelection = new MenuItem();
 -
 -  MenuItem delete = new MenuItem();
 -
 -  MenuItem copy = new MenuItem();
 -
 -  MenuItem cut = new MenuItem();
 -
 -  Menu pasteMenu = new Menu();
 -
 -  MenuItem pasteNew = new MenuItem();
 -
 -  MenuItem pasteThis = new MenuItem();
 -
 -  CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
 -
 -  MenuItem font = new MenuItem();
 -
 -  CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem scaleRight = new CheckboxMenuItem();
 -
 -  MenuItem modifyPID = new MenuItem();
 -
 -  MenuItem modifyConservation = new MenuItem();
 -
 -  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();
 -
 -  Menu calculate = new Menu();
 -
 -  MenuItem inputText = new MenuItem();
 -
 -  Menu helpMenu = new Menu();
 -
 -  MenuItem documentation = new MenuItem();
 -
 -  MenuItem about = new MenuItem();
 -
 -  CheckboxMenuItem seqLimits = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
 -
 -  Menu autoAnnMenu = new Menu();
 -
 -  CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
 -
 -  CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
 -
 -  private void jbInit() throws Exception
 -  {
 -
 -    setMenuBar(alignFrameMenuBar);
 -
 -    MenuItem item;
 -
 -    // dynamically fill save as menu with available formats
 -    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
 -    {
 -
 -      item = new MenuItem(
 -              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 -
 -      item.addActionListener(new java.awt.event.ActionListener()
 -      {
 -        @Override
 -        public void actionPerformed(ActionEvent e)
 -        {
 -          outputText_actionPerformed(e);
 -        }
 -      });
 -
 -      outputTextboxMenu.add(item);
 -    }
 -    closeMenuItem.addActionListener(this);
 -    loadApplication.addActionListener(this);
 -
 -    loadTree.addActionListener(this);
 -    loadAnnotations.addActionListener(this);
 -    outputFeatures.addActionListener(this);
 -    outputAnnotations.addActionListener(this);
 -    selectAllSequenceMenuItem.addActionListener(this);
 -    deselectAllSequenceMenuItem.addActionListener(this);
 -    invertSequenceMenuItem.addActionListener(this);
 -    remove2LeftMenuItem.setLabel("Remove Left");
 -    remove2LeftMenuItem.addActionListener(this);
 -    remove2RightMenuItem.setLabel("Remove Right");
 -    remove2RightMenuItem.addActionListener(this);
 -    removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
 -    removeGappedColumnMenuItem.addActionListener(this);
 -    removeAllGapsMenuItem.setLabel("Remove All Gaps");
 -    removeAllGapsMenuItem.addActionListener(this);
 -    viewBoxesMenuItem.setLabel("Boxes");
 -    viewBoxesMenuItem.setState(true);
 -    viewBoxesMenuItem.addItemListener(this);
 -    viewTextMenuItem.setLabel("Text");
 -    viewTextMenuItem.setState(true);
 -    viewTextMenuItem.addItemListener(this);
 -    sortPairwiseMenuItem.setLabel("by Pairwise Identity");
 -    sortPairwiseMenuItem.addActionListener(this);
 -    sortIDMenuItem.setLabel("by ID");
 -    sortIDMenuItem.addActionListener(this);
 -    sortLengthMenuItem.setLabel("by Length");
 -    sortLengthMenuItem.addActionListener(this);
 -    sortGroupMenuItem.setLabel("by Group");
 -    sortGroupMenuItem.addActionListener(this);
 -    removeRedundancyMenuItem.setLabel("Remove Redundancy...");
 -    removeRedundancyMenuItem.addActionListener(this);
 -    pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
 -    pairwiseAlignmentMenuItem.addActionListener(this);
 -    PCAMenuItem.setLabel("Principal Component Analysis");
 -    PCAMenuItem.addActionListener(this);
 -    averageDistanceTreeMenuItem
 -            .setLabel("Average Distance Using % Identity");
 -    averageDistanceTreeMenuItem.addActionListener(this);
 -    neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
 -    neighbourTreeMenuItem.addActionListener(this);
 -    statusBar.setBackground(Color.white);
 -    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 -    statusBar.setText("Status bar");
 -    outputTextboxMenu.setLabel("Output to Textbox");
 -    clustalColour.setLabel("Clustalx");
 -
 -    clustalColour.addActionListener(this);
 -    zappoColour.setLabel("Zappo");
 -    zappoColour.addActionListener(this);
 -    taylorColour.setLabel("Taylor");
 -    taylorColour.addActionListener(this);
 -    hydrophobicityColour.setLabel("Hydrophobicity");
 -    hydrophobicityColour.addActionListener(this);
 -    helixColour.setLabel("Helix Propensity");
 -    helixColour.addActionListener(this);
 -    strandColour.setLabel("Strand Propensity");
 -    strandColour.addActionListener(this);
 -    turnColour.setLabel("Turn Propensity");
 -    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);
 -    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);
 -    annotationPanelMenuItem.setLabel("Show Annotations");
 -    annotationPanelMenuItem.addItemListener(this);
 -    colourTextMenuItem.setLabel("Colour Text");
 -    colourTextMenuItem.addItemListener(this);
 -    displayNonconservedMenuItem.setLabel("Show nonconserved");
 -    displayNonconservedMenuItem.addItemListener(this);
 -    alProperties.addActionListener(this);
 -    overviewMenuItem.setLabel("Overview Window");
 -    overviewMenuItem.addActionListener(this);
 -    undoMenuItem.setEnabled(false);
 -    undoMenuItem.setLabel("Undo");
 -    undoMenuItem.addActionListener(this);
 -    redoMenuItem.setEnabled(false);
 -    redoMenuItem.setLabel("Redo");
 -    redoMenuItem.addActionListener(this);
 -    conservationMenuItem.setLabel("by Conservation");
 -    conservationMenuItem.addItemListener(this);
 -    noColourmenuItem.setLabel("None");
 -    noColourmenuItem.addActionListener(this);
 -    wrapMenuItem.setLabel("Wrap");
 -    wrapMenuItem.addItemListener(this);
 -    renderGapsMenuItem.setLabel("Show Gaps");
 -    renderGapsMenuItem.setState(true);
 -    renderGapsMenuItem.addItemListener(this);
 -    findMenuItem.setLabel("Find...");
 -    findMenuItem.addActionListener(this);
 -    abovePIDThreshold.setLabel("Above Identity Threshold");
 -    abovePIDThreshold.addItemListener(this);
 -    nucleotideColour.setLabel("Nucleotide");
 -    nucleotideColour.addActionListener(this);
 -    deleteGroups.setLabel("Undefine Groups");
 -    deleteGroups.addActionListener(this);
 -    grpsFromSelection.setLabel("Make Groups for selection");
 -    grpsFromSelection.addActionListener(this);
 -    copy.setLabel("Copy");
 -    copy.addActionListener(this);
 -    cut.setLabel("Cut");
 -    cut.addActionListener(this);
 -    delete.setLabel("Delete");
 -    delete.addActionListener(this);
 -    pasteMenu.setLabel("Paste");
 -    pasteNew.setLabel("To New Alignment");
 -    pasteNew.addActionListener(this);
 -    pasteThis.setLabel("Add To This Alignment");
 -    pasteThis.addActionListener(this);
 -    applyToAllGroups.setLabel("Apply Colour To All Groups");
 -    applyToAllGroups.setState(true);
 -    applyToAllGroups.addItemListener(this);
 -    font.setLabel("Font...");
 -    font.addActionListener(this);
 -    scaleAbove.setLabel("Scale Above");
 -    scaleAbove.setState(true);
 -    scaleAbove.setEnabled(false);
 -    scaleAbove.addItemListener(this);
 -    scaleLeft.setEnabled(false);
 -    scaleLeft.setState(true);
 -    scaleLeft.setLabel("Scale Left");
 -    scaleLeft.addItemListener(this);
 -    scaleRight.setEnabled(false);
 -    scaleRight.setState(true);
 -    scaleRight.setLabel("Scale Right");
 -    scaleRight.addItemListener(this);
 -    modifyPID.setLabel("Modify Identity Threshold...");
 -    modifyPID.addActionListener(this);
 -    modifyConservation.setLabel("Modify Conservation Threshold...");
 -    modifyConservation.addActionListener(this);
 -    sortByTreeMenu.setLabel("By Tree Order");
 -    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");
 -    centreColumnLabelFlag.addItemListener(this);
 -    followMouseOverFlag.setLabel("Automatic Scrolling");
 -    followMouseOverFlag.addItemListener(this);
 -    helpMenu.setLabel("Help");
 -    documentation.setLabel("Documentation");
 -    documentation.addActionListener(this);
 -
 -    about.setLabel("About...");
 -    about.addActionListener(this);
 -    seqLimits.setState(true);
 -    seqLimits.setLabel("Show Sequence Limits");
 -    seqLimits.addItemListener(this);
 -    featureSettings.setLabel("Feature Settings...");
 -    featureSettings.addActionListener(this);
 -    sequenceFeatures.setLabel("Sequence Features");
 -    sequenceFeatures.addItemListener(this);
 -    sequenceFeatures.setState(false);
 -    annotationColour.setLabel("by Annotation...");
 -    annotationColour.addActionListener(this);
 -    invertSequenceMenuItem.setLabel("Invert Sequence Selection");
 -    invertColSel.setLabel("Invert Column Selection");
 -    menu1.setLabel("Show");
 -    showColumns.setLabel("All Columns ");
 -    showSeqs.setLabel("All Sequences");
 -    menu2.setLabel("Hide");
 -    hideColumns.setLabel("Selected Columns");
 -    hideSequences.setLabel("Selected Sequences");
 -    hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
 -    hideAllSelection.setLabel("Selected Region");
 -    showAllHidden.setLabel("All Sequences and Columns");
 -    showGroupConsensus.setLabel("Group Consensus");
 -    showGroupConservation.setLabel("Group Conservation");
 -    showConsensusHistogram.setLabel("Show Consensus Histogram");
 -    showSequenceLogo.setLabel("Show Consensus Logo");
 -    normSequenceLogo.setLabel("Normalise Consensus Logo");
 -    applyAutoAnnotationSettings.setLabel("Apply to all groups");
 -    applyAutoAnnotationSettings.setState(true);
 -    autoAnnMenu.setLabel("Autocalculated Annotation");
 -
 -    invertColSel.addActionListener(this);
 -    showColumns.addActionListener(this);
 -    showSeqs.addActionListener(this);
 -    hideColumns.addActionListener(this);
 -    hideSequences.addActionListener(this);
 -    hideAllButSelection.addActionListener(this);
 -    hideAllSelection.addActionListener(this);
 -    showAllHidden.addActionListener(this);
 -    showGroupConsensus.addItemListener(this);
 -    showGroupConservation.addItemListener(this);
 -    showConsensusHistogram.addItemListener(this);
 -    showSequenceLogo.addItemListener(this);
 -    normSequenceLogo.addItemListener(this);
 -
 -    applyAutoAnnotationSettings.addItemListener(this);
 -    formatMenu.setLabel("Format");
 -    selectMenu.setLabel("Select");
 -    newView.setLabel("New View");
 -    newView.addActionListener(this);
 -    alignFrameMenuBar.add(fileMenu);
 -    alignFrameMenuBar.add(editMenu);
 -    alignFrameMenuBar.add(selectMenu);
 -    alignFrameMenuBar.add(viewMenu);
 -    alignFrameMenuBar.add(formatMenu);
 -    alignFrameMenuBar.add(colourMenu);
 -    alignFrameMenuBar.add(calculateMenu);
 -    alignFrameMenuBar.add(helpMenu);
 -
 -    fileMenu.add(inputText);
 -    fileMenu.add(loadTree);
 -    fileMenu.add(loadAnnotations);
 -
 -    fileMenu.addSeparator();
 -    fileMenu.add(outputTextboxMenu);
 -    fileMenu.add(outputFeatures);
 -    fileMenu.add(outputAnnotations);
 -
 -    if (jalviewServletURL != null)
 -    {
 -      fileMenu.add(loadApplication);
 -    }
 -
 -    fileMenu.addSeparator();
 -    fileMenu.add(closeMenuItem);
 -
 -    editMenu.add(undoMenuItem);
 -    editMenu.add(redoMenuItem);
 -    editMenu.add(cut);
 -    editMenu.add(copy);
 -    editMenu.add(pasteMenu);
 -    editMenu.add(delete);
 -    editMenu.addSeparator();
 -    editMenu.add(remove2LeftMenuItem);
 -    editMenu.add(remove2RightMenuItem);
 -    editMenu.add(removeGappedColumnMenuItem);
 -    editMenu.add(removeAllGapsMenuItem);
 -    editMenu.add(removeRedundancyMenuItem);
 -    viewMenu.add(newView);
 -    viewMenu.addSeparator();
 -    viewMenu.add(menu1);
 -    viewMenu.add(menu2);
 -    viewMenu.addSeparator();
 -    viewMenu.add(followMouseOverFlag);
 -    viewMenu.add(annotationPanelMenuItem);
 -    autoAnnMenu.add(applyAutoAnnotationSettings);
 -    autoAnnMenu.add(showConsensusHistogram);
 -    autoAnnMenu.add(showSequenceLogo);
 -    autoAnnMenu.add(normSequenceLogo);
 -    autoAnnMenu.addSeparator();
 -    autoAnnMenu.add(showGroupConservation);
 -    autoAnnMenu.add(showGroupConsensus);
 -    viewMenu.add(autoAnnMenu);
 -    viewMenu.addSeparator();
 -    viewMenu.add(sequenceFeatures);
 -    viewMenu.add(featureSettings);
 -    viewMenu.addSeparator();
 -    viewMenu.add(alProperties);
 -    viewMenu.addSeparator();
 -    viewMenu.add(overviewMenuItem);
 -    colourMenu.add(applyToAllGroups);
 -    colourMenu.addSeparator();
 -    colourMenu.add(noColourmenuItem);
 -    colourMenu.add(clustalColour);
 -    colourMenu.add(BLOSUM62Colour);
 -    colourMenu.add(PIDColour);
 -    colourMenu.add(zappoColour);
 -    colourMenu.add(taylorColour);
 -    colourMenu.add(hydrophobicityColour);
 -    colourMenu.add(helixColour);
 -    colourMenu.add(strandColour);
 -    colourMenu.add(turnColour);
 -    colourMenu.add(buriedColour);
 -    colourMenu.add(nucleotideColour);
 -    colourMenu.add(purinePyrimidineColour);
 -    colourMenu.add(tcoffeeColour);
 -    colourMenu.add(userDefinedColour);
 -    colourMenu.addSeparator();
 -    colourMenu.add(conservationMenuItem);
 -    colourMenu.add(modifyConservation);
 -    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);
 -    sort.add(sortIDMenuItem);
 -    sort.add(sortLengthMenuItem);
 -    sort.add(sortByTreeMenu);
 -    sort.add(sortGroupMenuItem);
 -    sort.add(sortPairwiseMenuItem);
 -    calculate.add(averageDistanceTreeMenuItem);
 -    calculate.add(neighbourTreeMenuItem);
 -    calculate.add(avDistanceTreeBlosumMenuItem);
 -    calculate.add(njTreeBlosumMenuItem);
 -    helpMenu.add(documentation);
 -    helpMenu.add(about);
 -    menu1.add(showColumns);
 -    menu1.add(showSeqs);
 -    menu1.add(showAllHidden);
 -    menu2.add(hideColumns);
 -    menu2.add(hideSequences);
 -    menu2.add(hideAllSelection);
 -    menu2.add(hideAllButSelection);
 -    formatMenu.add(font);
 -    formatMenu.add(seqLimits);
 -    formatMenu.add(wrapMenuItem);
 -    formatMenu.add(scaleAbove);
 -    formatMenu.add(scaleLeft);
 -    formatMenu.add(scaleRight);
 -    formatMenu.add(viewBoxesMenuItem);
 -    formatMenu.add(viewTextMenuItem);
 -    formatMenu.add(colourTextMenuItem);
 -    formatMenu.add(displayNonconservedMenuItem);
 -    formatMenu.add(renderGapsMenuItem);
 -    formatMenu.add(centreColumnLabelFlag);
 -    selectMenu.add(findMenuItem);
 -    selectMenu.addSeparator();
 -    selectMenu.add(selectAllSequenceMenuItem);
 -    selectMenu.add(deselectAllSequenceMenuItem);
 -    selectMenu.add(invertSequenceMenuItem);
 -    selectMenu.add(invertColSel);
 -    selectMenu.add(grpsFromSelection);
 -    selectMenu.add(deleteGroups);
 -
 -  }
 -
 -  MenuItem featureSettings = new MenuItem();
 -
 -  CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
 -
 -  MenuItem annotationColour = new MenuItem();
 -
 -  MenuItem invertColSel = new MenuItem();
 -
 -  Menu menu1 = new Menu();
 -
 -  MenuItem showColumns = new MenuItem();
 -
 -  MenuItem showSeqs = new MenuItem();
 -
 -  Menu menu2 = new Menu();
 -
 -  MenuItem hideColumns = new MenuItem();
 -
 -  MenuItem hideSequences = new MenuItem();
 -
 -  MenuItem hideAllButSelection = new MenuItem();
 -
 -  MenuItem hideAllSelection = new MenuItem();
 -
 -  MenuItem showAllHidden = new MenuItem();
 -
 -  Menu formatMenu = new Menu();
 -
 -  Menu selectMenu = new Menu();
 -
 -  MenuItem newView = new MenuItem();
 -
 -  /**
 -   * Attach the alignFrame panels after embedding menus, if necessary. This used
 -   * to be called setEmbedded, but is now creates the dropdown menus in a
 -   * platform independent manner to avoid OSX/Mac menu appendage daftness.
 -   * 
 -   * @param reallyEmbedded
 -   *          true to attach the view to the applet area on the page rather than
 -   *          in a new window
 -   */
 -  public void createAlignFrameWindow(boolean reallyEmbedded, String title)
 -  {
 -    if (reallyEmbedded)
 -    {
 -      // ////
 -      // Explicly build the embedded menu panel for the on-page applet
 -      //
 -      // view cannot be closed if its actually on the page
 -      fileMenu.remove(closeMenuItem);
 -      fileMenu.remove(3); // Remove Seperator
 -      embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
 -              Font.PLAIN, 10, false); // use our own fonts.
 -      // and actually add the components to the applet area
 -      viewport.applet.setLayout(new BorderLayout());
 -      viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
 -      viewport.applet.add(statusBar, BorderLayout.SOUTH);
 -      alignPanel.setSize(viewport.applet.getSize().width,
 -              viewport.applet.getSize().height - embeddedMenu.HEIGHT
 -                      - statusBar.HEIGHT);
 -      viewport.applet.add(alignPanel, BorderLayout.CENTER);
 -      final AlignFrame me = this;
 -      viewport.applet.addFocusListener(new FocusListener()
 -      {
 -
 -        @Override
 -        public void focusLost(FocusEvent e)
 -        {
 -          if (me.viewport.applet.currentAlignFrame == me)
 -          {
 -            me.viewport.applet.currentAlignFrame = null;
 -          }
 -        }
 -
 -        @Override
 -        public void focusGained(FocusEvent e)
 -        {
 -          me.viewport.applet.currentAlignFrame = me;
 -        }
 -      });
 -      viewport.applet.validate();
 -    }
 -    else
 -    {
 -      // //////
 -      // test and embed menu bar if necessary.
 -      //
 -      if (embedMenuIfNeeded(alignPanel))
 -      {
 -        // adjust for status bar height too
 -        alignPanel.setSize(getSize().width, getSize().height
 -                - statusBar.HEIGHT);
 -      }
 -      add(statusBar, BorderLayout.SOUTH);
 -      add(alignPanel, BorderLayout.CENTER);
 -      // and register with the applet so it can pass external API calls to us
 -      jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
 -              DEFAULT_HEIGHT);
 -    }
 -  }
 -
 -  /**
 -   * create a new binding between structures in an existing jmol viewer instance
 -   * and an alignpanel with sequences that have existing PDBFile entries. Note,
 -   * this does not open a new Jmol window, or modify the display of the
 -   * structures in the original jmol window. Note This method doesn't work
 -   * without an additional javascript library to exchange messages between the
 -   * distinct applets. See http://issues.jalview.org/browse/JAL-621
 -   * 
 -   * @param viewer
 -   *          JmolViewer instance
 -   * @param sequenceIds
 -   *          - sequence Ids to search for associations
 -   */
 -  public SequenceStructureBinding addStructureViewInstance(
 -          Object jmolviewer, String[] sequenceIds)
 -  {
 -    org.jmol.api.JmolViewer viewer = null;
 -    try
 -    {
 -      viewer = (org.jmol.api.JmolViewer) jmolviewer;
 -    } catch (ClassCastException ex)
 -    {
 -      System.err.println("Unsupported viewer object :"
 -              + jmolviewer.getClass());
 -    }
 -    if (viewer == null)
 -    {
 -      System.err.println("Can't use this object as a structure viewer:"
 -              + jmolviewer.getClass());
 -      return null;
 -    }
 -    SequenceI[] seqs = null;
 -    if (sequenceIds == null || sequenceIds.length == 0)
 -    {
 -      seqs = viewport.getAlignment().getSequencesArray();
 -    }
 -    else
 -    {
 -      Vector sqi = new Vector();
 -      AlignmentI al = viewport.getAlignment();
 -      for (int sid = 0; sid < sequenceIds.length; sid++)
 -      {
 -        SequenceI sq = al.findName(sequenceIds[sid]);
 -        if (sq != null)
 -        {
 -          sqi.addElement(sq);
 -        }
 -      }
 -      if (sqi.size() > 0)
 -      {
 -        seqs = new SequenceI[sqi.size()];
 -        for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
 -        {
 -          seqs[sid] = (SequenceI) sqi.elementAt(sid);
 -        }
 -      }
 -      else
 -      {
 -        return null;
 -      }
 -    }
 -    ExtJmol jmv = null;
 -    // TODO: search for a jmv that involves viewer
 -    if (jmv == null)
 -    { // create a new viewer/jalview binding.
 -      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
 -      { seqs });
 -    }
 -    return jmv;
 -
 -  }
 -
 -  /**
 -   * bind a pdb file to a sequence in the current view
 -   * 
 -   * @param sequenceId
 -   *          - sequenceId within the dataset.
 -   * @param pdbEntryString
 -   *          - the short name for the PDB file
 -   * @param pdbFile
 -   *          - pdb file - either a URL or a valid PDB file.
 -   * @return true if binding was as success TODO: consider making an exception
 -   *         structure for indicating when PDB parsing or sequenceId location
 -   *         fails.
 -   */
 -  public boolean addPdbFile(String sequenceId, String pdbEntryString,
 -          String pdbFile)
 -  {
 -    SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
 -    boolean needtoadd = false;
 -    if (toaddpdb != null)
 -    {
 -      Vector pdbe = toaddpdb.getPDBId();
 -      PDBEntry pdbentry = null;
 -      if (pdbe != null && pdbe.size() > 0)
 -      {
 -        for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
 -        {
 -          pdbentry = (PDBEntry) pdbe.elementAt(pe);
 -          if (!pdbentry.getId().equals(pdbEntryString)
 -                  && !pdbentry.getFile().equals(pdbFile))
 -          {
 -            pdbentry = null;
 -          }
 -          else
 -          {
 -            continue;
 -          }
 -        }
 -      }
 -      if (pdbentry == null)
 -      {
 -        pdbentry = new PDBEntry();
 -        pdbentry.setId(pdbEntryString);
 -        pdbentry.setFile(pdbFile);
 -        needtoadd = true; // add this new entry to sequence.
 -      }
 -      // resolve data source
 -      // TODO: this code should be a refactored to an io package
 -      String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
 -      if (protocol == null)
 -      {
 -        return false;
 -      }
 -      if (needtoadd)
 -      {
 -        // make a note of the access mode and add
 -        if (pdbentry.getProperty() == null)
 -        {
 -          pdbentry.setProperty(new Hashtable());
 -        }
 -        pdbentry.getProperty().put("protocol", protocol);
 -        toaddpdb.addPDBId(pdbentry);
 -      }
 -    }
 -    return true;
 -  }
 -
 -  private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
 -  {
 -    if (seqs != null)
 -    {
 -      Vector sequences = new Vector();
 -      for (int i = 0; i < seqs.length; i++)
 -      {
 -        if (seqs[i] != null)
 -        {
 -          sequences.addElement(new Object[]
 -          { seqs[i], (chains != null) ? chains[i] : null });
 -        }
 -      }
 -      seqs = new SequenceI[sequences.size()];
 -      chains = new String[sequences.size()];
 -      for (int i = 0, isize = sequences.size(); i < isize; i++)
 -      {
 -        Object[] oj = (Object[]) sequences.elementAt(i);
 -
 -        seqs[i] = (SequenceI) oj[0];
 -        chains[i] = (String) oj[1];
 -      }
 -    }
 -    return new Object[]
 -    { seqs, chains };
 -
 -  }
 -
 -  public void newStructureView(JalviewLite applet, PDBEntry pdb,
 -          SequenceI[] seqs, String[] chains, String protocol)
 -  {
 -    // Scrub any null sequences from the array
 -    Object[] sqch = cleanSeqChainArrays(seqs, chains);
 -    seqs = (SequenceI[]) sqch[0];
 -    chains = (String[]) sqch[1];
 -    if (seqs == null || seqs.length == 0)
 -    {
 -      System.err
 -              .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
 -    }
 -    if (protocol == null || protocol.trim().length() == 0
 -            || protocol.equals("null"))
 -    {
 -      protocol = (String) pdb.getProperty().get("protocol");
 -      if (protocol == null)
 -      {
 -        System.err.println("Couldn't work out protocol to open structure: "
 -                + pdb.getId());
 -        return;
 -      }
 -    }
 -    if (applet.useXtrnalSviewer)
 -    {
 -      // register the association(s) and quit, don't create any windows.
 -      if (StructureSelectionManager.getStructureSelectionManager(applet)
 -              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
 -      {
 -        System.err.println("Failed to map " + pdb.getFile() + " ("
 -                + protocol + ") to any sequences");
 -      }
 -      return;
 -    }
 -    if (applet.isAlignPdbStructures() && applet.jmolAvailable)
 -    {
 -      // can only do alignments with Jmol
 -      // find the last jmol window assigned to this alignment
 -      jalview.appletgui.AppletJmol ajm = null, tajm;
 -      Vector jmols = applet
 -              .getAppletWindow(jalview.appletgui.AppletJmol.class);
 -      for (int i = 0, iSize = jmols.size(); i < iSize; i++)
 -      {
 -        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
 -        if (tajm.ap.alignFrame == this)
 -        {
 -          ajm = tajm;
 -          break;
 -        }
 -      }
 -      if (ajm != null)
 -      {
 -        System.err
 -                .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
 -        // try and add the pdb structure
 -        // ajm.addS
 -        ajm = null;
 -      }
 -    }
 -    // otherwise, create a new window
 -    if (applet.jmolAvailable)
 -    {
 -      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
 -              protocol);
 -      applet.lastFrameX += 40;
 -      applet.lastFrameY += 40;
 -    }
 -    else
 -    {
 -      new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
 -    }
 -
 -  }
 -
 -  public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
 -          SequenceI[][] seqs, String[][] chains, String[] protocols)
 -  {
 -    // TODO Auto-generated method stub
 -    System.err.println("Aligned Structure View: Not yet implemented.");
 -  }
 -
 -  /**
 -   * modify the current selection, providing the user has not made a selection
 -   * already.
 -   * 
 -   * @param sel
 -   *          - sequences from this alignment
 -   * @param csel
 -   *          - columns to be selected on the alignment
 -   */
 -  public void select(SequenceGroup sel, ColumnSelection csel)
 -  {
 -    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;
 -  }
 -
 -}
 +/*
-  * 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
-  *
++ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
++ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
++ * 
 + * This file is part of Jalview.
-  *
++ * 
 + * Jalview is free software: you can redistribute it and/or
-  * modify it under the terms of the GNU General Public License
++ * modify it under the terms of the GNU General Public License 
 + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-  *
-  * Jalview is distributed in the hope that it will be useful, but
-  * WITHOUT ANY WARRANTY; without even the implied warranty
-  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
++ *  
++ * Jalview is distributed in the hope that it will be useful, but 
++ * WITHOUT ANY WARRANTY; without even the implied warranty 
++ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 + * PURPOSE.  See the GNU General Public License for more details.
-  *
++ * 
 + * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 + */
 +package jalview.appletgui;
 +
 +import jalview.analysis.AAFrequency;
 +import jalview.analysis.AlignmentSorter;
 +import jalview.analysis.Conservation;
 +import jalview.api.SequenceStructureBinding;
 +import jalview.bin.JalviewLite;
 +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.SequenceCollectionI;
 +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.RNAInteractionColourScheme;
 +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;
 +
 +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;
 +
 +import javax.xml.parsers.ParserConfigurationException;
 +
 +import org.xml.sax.SAXException;
 +
 +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 +
- public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemListener, KeyListener
++public class AlignFrame extends EmbmenuFrame implements ActionListener,
++        ItemListener, KeyListener
 +{
 +  public AlignmentPanel alignPanel;
 +
 +  public AlignViewport viewport;
 +
 +  int DEFAULT_WIDTH = 700;
 +
 +  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");
 +    }
 +
 +    try
 +    {
 +      jbInit();
 +    } catch (Exception ex)
 +    {
 +      ex.printStackTrace();
 +    }
 +
 +    viewport = new AlignViewport(al, applet);
 +    alignPanel = new AlignmentPanel(this, viewport);
 +
 +    viewport.updateConservation(alignPanel);
 +    viewport.updateConsensus(alignPanel);
 +
 +    annotationPanelMenuItem.setState(viewport.showAnnotation);
 +    displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 +    followMouseOverFlag.setState(viewport.getFollowHighlight());
 +    showGroupConsensus.setState(viewport.isShowGroupConsensus());
 +    showGroupConservation.setState(viewport.isShowGroupConservation());
 +    showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 +    showSequenceLogo.setState(viewport.isShowSequenceLogo());
++    normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 +
 +    seqLimits.setState(viewport.showJVSuffix);
 +
 +    if (applet != null)
 +    {
 +      String param = applet.getParameter("sortBy");
 +      if (param != null)
 +      {
 +        if (param.equalsIgnoreCase("Id"))
 +        {
 +          sortIDMenuItem_actionPerformed();
 +        }
 +        else if (param.equalsIgnoreCase("Pairwise Identity"))
 +        {
 +          sortPairwiseMenuItem_actionPerformed();
 +        }
 +        else if (param.equalsIgnoreCase("Length"))
 +        {
 +          sortLengthMenuItem_actionPerformed();
 +        }
 +      }
 +
 +      param = applet.getParameter("wrap");
 +      if (param != null)
 +      {
 +        if (param.equalsIgnoreCase("true"))
 +        {
 +          wrapMenuItem.setState(true);
 +          wrapMenuItem_actionPerformed();
 +        }
 +      }
 +      param = applet.getParameter("centrecolumnlabels");
 +      if (param != null)
 +      {
 +        centreColumnLabelFlag.setState(true);
 +        centreColumnLabelFlag_stateChanged();
 +      }
 +      try
 +      {
 +        param = applet.getParameter("windowWidth");
 +        if (param != null)
 +        {
 +          int width = Integer.parseInt(param);
 +          DEFAULT_WIDTH = width;
 +        }
 +        param = applet.getParameter("windowHeight");
 +        if (param != null)
 +        {
 +          int height = Integer.parseInt(param);
 +          DEFAULT_HEIGHT = height;
 +        }
 +      } catch (Exception ex)
 +      {
 +      }
 +
 +    }
 +    if (viewport.getAlignment().isNucleotide())
 +    {
 +      viewport.updateStrucConsensus(alignPanel);
 +      if (viewport.getAlignment().hasRNAStructure())
 +      {
 +        RNAHelixColour.setEnabled(true);
 +      }
-       else {
++      else
++      {
 +        RNAHelixColour.setEnabled(false);
 +      }
-     } else {
++    }
++    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
 +    this.addKeyListener(this);
 +    alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 +    alignPanel.idPanel.idCanvas.addKeyListener(this);
 +    alignPanel.scalePanel.addKeyListener(this);
 +    alignPanel.annotationPanel.addKeyListener(this);
 +    alignPanel.annotationPanelHolder.addKeyListener(this);
 +    alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 +    alignPanel.alabels.addKeyListener(this);
 +    createAlignFrameWindow(embedded, title);
 +
 +    validate();
 +    alignPanel.adjustAnnotationHeight();
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  public AlignViewport getAlignViewport()
 +  {
 +    return viewport;
 +  }
 +
 +  public SeqCanvas getSeqcanvas()
 +  {
 +    return alignPanel.seqPanel.seqCanvas;
 +  }
 +
 +  /**
 +   * 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 file
++   *          file URL, content, or other resolvable path
++   * @param type
++   *          is protocol for accessing data referred to by file
 +   */
 +
 +  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
++   * 
++   * @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)
++  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.
++    // 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.getAlignment(),
-                       alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
-                       featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
++              .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
++                      .getFeatureRenderer().featureColours, featureLinks,
++                      true, viewport.applet.getDefaultParameter(
++                              "relaxedidmatch", false));
 +    } catch (Exception ex)
 +    {
 +      ex.printStackTrace();
 +    }
 +
 +    if (featuresFile)
 +    {
 +      if (featureLinks.size() > 0)
 +      {
 +        alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 +      }
 +      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;
 +  }
 +
 +  @Override
 +  public void keyPressed(KeyEvent evt)
 +  {
 +    if (viewport.cursorMode
 +            && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 +                    .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 +                    .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 +            && Character.isDigit(evt.getKeyChar()))
 +      alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 +
 +    switch (evt.getKeyCode())
 +    {
 +    case 27: // escape key
 +      deselectAllSequenceMenuItem_actionPerformed();
 +
 +      alignPanel.alabels.cancelDrag();
 +      break;
 +    case KeyEvent.VK_X:
 +      if (evt.isControlDown() || evt.isMetaDown())
 +      {
 +        cut_actionPerformed();
 +      }
 +      break;
 +    case KeyEvent.VK_C:
 +      if (viewport.cursorMode && !evt.isControlDown())
 +      {
 +        alignPanel.seqPanel.setCursorColumn();
 +      }
 +      if (evt.isControlDown() || evt.isMetaDown())
 +      {
 +        copy_actionPerformed();
 +      }
 +      break;
 +    case KeyEvent.VK_V:
 +      if (evt.isControlDown())
 +      {
 +        paste(evt.isShiftDown());
 +      }
 +      break;
 +    case KeyEvent.VK_A:
 +      if (evt.isControlDown() || evt.isMetaDown())
 +      {
 +        selectAllSequenceMenuItem_actionPerformed();
 +      }
 +      break;
 +    case KeyEvent.VK_DOWN:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.moveCursor(0, 1);
 +      }
 +      else
 +      {
 +        moveSelectedSequences(false);
 +      }
 +      break;
 +
 +    case KeyEvent.VK_UP:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.moveCursor(0, -1);
 +      }
 +      else
 +      {
 +        moveSelectedSequences(true);
 +      }
 +      break;
 +
 +    case KeyEvent.VK_LEFT:
 +      if (evt.isAltDown() || !viewport.cursorMode)
 +        slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 +      else
 +        alignPanel.seqPanel.moveCursor(-1, 0);
 +      break;
 +
 +    case KeyEvent.VK_RIGHT:
 +      if (evt.isAltDown() || !viewport.cursorMode)
 +        slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 +      else
 +        alignPanel.seqPanel.moveCursor(1, 0);
 +      break;
 +
 +    case KeyEvent.VK_SPACE:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 +                || evt.isShiftDown() || evt.isAltDown());
 +      }
 +      break;
 +
 +    case KeyEvent.VK_DELETE:
 +    case KeyEvent.VK_BACK_SPACE:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 +                || evt.isShiftDown() || evt.isAltDown());
 +      }
 +      else
 +      {
 +        cut_actionPerformed();
 +        alignPanel.seqPanel.seqCanvas.repaint();
 +      }
 +      break;
 +
 +    case KeyEvent.VK_S:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.setCursorRow();
 +      }
 +      break;
 +    case KeyEvent.VK_P:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.setCursorPosition();
 +      }
 +      break;
 +
 +    case KeyEvent.VK_ENTER:
 +    case KeyEvent.VK_COMMA:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.setCursorRowAndColumn();
 +      }
 +      break;
 +
 +    case KeyEvent.VK_Q:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 +      }
 +      break;
 +    case KeyEvent.VK_M:
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 +      }
 +      break;
 +
 +    case KeyEvent.VK_F2:
 +      viewport.cursorMode = !viewport.cursorMode;
 +      statusBar.setText("Keyboard editing mode is "
 +              + (viewport.cursorMode ? "on" : "off"));
 +      if (viewport.cursorMode)
 +      {
 +        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 +        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 +      }
 +      break;
 +
 +    case KeyEvent.VK_F:
 +      if (evt.isControlDown())
 +      {
 +        findMenuItem_actionPerformed();
 +      }
 +      break;
 +
 +    case KeyEvent.VK_H:
 +    {
 +      boolean toggleSeqs = !evt.isControlDown();
 +      boolean toggleCols = !evt.isShiftDown();
 +      toggleHiddenRegions(toggleSeqs, toggleCols);
 +      break;
 +    }
 +
 +    case KeyEvent.VK_PAGE_UP:
 +      if (viewport.wrapAlignment)
 +      {
 +        alignPanel.scrollUp(true);
 +      }
 +      else
 +      {
 +        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 +                - viewport.endSeq + viewport.startSeq);
 +      }
 +      break;
 +
 +    case KeyEvent.VK_PAGE_DOWN:
 +      if (viewport.wrapAlignment)
 +      {
 +        alignPanel.scrollUp(false);
 +      }
 +      else
 +      {
 +        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 +                + viewport.endSeq - viewport.startSeq);
 +      }
 +      break;
 +
 +    case KeyEvent.VK_Z:
 +      if (evt.isControlDown())
 +      {
 +        undoMenuItem_actionPerformed();
 +      }
 +      break;
 +
 +    case KeyEvent.VK_Y:
 +      if (evt.isControlDown())
 +      {
 +        redoMenuItem_actionPerformed();
 +      }
 +      break;
 +
 +    case KeyEvent.VK_L:
 +      if (evt.isControlDown())
 +      {
 +        trimAlignment(true);
 +      }
 +      break;
 +
 +    case KeyEvent.VK_R:
 +      if (evt.isControlDown())
 +      {
 +        trimAlignment(false);
 +      }
 +      break;
 +
 +    case KeyEvent.VK_E:
 +      if (evt.isControlDown())
 +      {
 +        if (evt.isShiftDown())
 +        {
 +          this.removeAllGapsMenuItem_actionPerformed();
 +        }
 +        else
 +        {
 +          removeGappedColumnMenuItem_actionPerformed();
 +        }
 +      }
 +      break;
 +    case KeyEvent.VK_I:
 +      if (evt.isControlDown())
 +      {
 +        if (evt.isAltDown())
 +        {
 +          invertColSel_actionPerformed();
 +        }
 +        else
 +        {
 +          invertSequenceMenuItem_actionPerformed();
 +        }
 +      }
 +      break;
 +
 +    case KeyEvent.VK_U:
 +      if (evt.isControlDown())
 +      {
 +        this.deleteGroups_actionPerformed();
 +      }
 +      break;
 +
 +    case KeyEvent.VK_T:
 +      if (evt.isControlDown())
 +      {
 +        newView(null);
 +      }
 +      break;
 +
 +    }
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  /**
 +   * called by key handler and the hide all/show all menu items
-    *
++   * 
 +   * @param toggleSeqs
 +   * @param toggleCols
 +   */
 +  private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 +  {
 +    boolean hide = false;
 +    SequenceGroup sg = viewport.getSelectionGroup();
 +    if (!toggleSeqs && !toggleCols)
 +    {
 +      // Hide everything by the current selection - this is a hack - we do the
 +      // invert and then hide
 +      // first check that there will be visible columns after the invert.
-       if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
-               .getSelected().size() > 0)
++      if ((viewport.getColumnSelection() != null
++              && viewport.getColumnSelection().getSelected() != null && viewport
++              .getColumnSelection().getSelected().size() > 0)
 +              || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 +                      .getEndRes()))
 +      {
 +        // now invert the sequence set, if required - empty selection implies
 +        // that no hiding is required.
 +        if (sg != null)
 +        {
 +          invertSequenceMenuItem_actionPerformed();
 +          sg = viewport.getSelectionGroup();
 +          toggleSeqs = true;
 +
 +        }
 +        viewport.expandColSelection(sg, true);
 +        // finally invert the column selection and get the new sequence
 +        // selection and indicate it should be hidden.
 +        invertColSel_actionPerformed();
 +        toggleCols = true;
 +      }
 +    }
 +
 +    if (toggleSeqs)
 +    {
 +      if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 +      {
 +        hide = true;
 +        viewport.hideAllSelectedSeqs();
 +      }
-       else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
++      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
++              .size() > 0))
 +      {
 +        viewport.showAllHiddenSeqs();
 +      }
 +    }
 +
 +    if (toggleCols)
 +    {
 +      if (viewport.getColumnSelection().getSelected().size() > 0)
 +      {
 +        viewport.hideSelectedColumns();
 +        if (!toggleSeqs)
 +        {
 +          viewport.setSelectionGroup(sg);
 +        }
 +      }
 +      else if (!hide)
 +      {
 +        viewport.showAllHiddenColumns();
 +      }
 +    }
 +  }
 +
 +  @Override
 +  public void keyReleased(KeyEvent evt)
 +  {
 +  }
 +
 +  @Override
 +  public void keyTyped(KeyEvent evt)
 +  {
 +  }
 +
 +  @Override
 +  public void itemStateChanged(ItemEvent evt)
 +  {
 +    if (evt.getSource() == displayNonconservedMenuItem)
 +    {
 +      displayNonconservedMenuItem_actionPerformed();
 +    }
 +    else if (evt.getSource() == colourTextMenuItem)
 +    {
 +      colourTextMenuItem_actionPerformed();
 +    }
 +    else if (evt.getSource() == wrapMenuItem)
 +    {
 +      wrapMenuItem_actionPerformed();
 +    }
 +    else if (evt.getSource() == scaleAbove)
 +    {
 +      viewport.setScaleAboveWrapped(scaleAbove.getState());
 +    }
 +    else if (evt.getSource() == scaleLeft)
 +    {
 +      viewport.setScaleLeftWrapped(scaleLeft.getState());
 +    }
 +    else if (evt.getSource() == scaleRight)
 +    {
 +      viewport.setScaleRightWrapped(scaleRight.getState());
 +    }
 +    else if (evt.getSource() == seqLimits)
 +    {
 +      seqLimits_itemStateChanged();
 +    }
 +    else if (evt.getSource() == viewBoxesMenuItem)
 +    {
 +      viewport.setShowBoxes(viewBoxesMenuItem.getState());
 +    }
 +    else if (evt.getSource() == viewTextMenuItem)
 +    {
 +      viewport.setShowText(viewTextMenuItem.getState());
 +    }
 +    else if (evt.getSource() == renderGapsMenuItem)
 +    {
 +      viewport.setRenderGaps(renderGapsMenuItem.getState());
 +    }
 +    else if (evt.getSource() == annotationPanelMenuItem)
 +    {
 +      viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 +      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 +    }
 +    else if (evt.getSource() == sequenceFeatures)
 +    {
 +      viewport.showSequenceFeatures(sequenceFeatures.getState());
 +      alignPanel.seqPanel.seqCanvas.repaint();
 +    }
 +    else if (evt.getSource() == conservationMenuItem)
 +    {
 +      conservationMenuItem_actionPerformed();
 +    }
 +    else if (evt.getSource() == abovePIDThreshold)
 +    {
 +      abovePIDThreshold_actionPerformed();
 +    }
 +    else if (evt.getSource() == applyToAllGroups)
 +    {
 +      viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 +    }
 +    else if (evt.getSource() == autoCalculate)
 +    {
 +      viewport.autoCalculateConsensus = autoCalculate.getState();
 +    }
 +    else if (evt.getSource() == sortByTree)
 +    {
 +      viewport.sortByTree = sortByTree.getState();
 +    }
 +    else if (evt.getSource() == this.centreColumnLabelFlag)
 +    {
 +      centreColumnLabelFlag_stateChanged();
 +    }
 +    else if (evt.getSource() == this.followMouseOverFlag)
 +    {
 +      mouseOverFlag_stateChanged();
 +    }
 +    else if (evt.getSource() == showGroupConsensus)
 +    {
 +      showGroupConsensus_actionPerformed();
 +    }
 +    else if (evt.getSource() == showGroupConservation)
 +    {
 +      showGroupConservation_actionPerformed();
 +    }
 +    else if (evt.getSource() == showSequenceLogo)
 +    {
 +      showSequenceLogo_actionPerformed();
 +    }
++    else if (evt.getSource() == normSequenceLogo)
++    {
++      normSequenceLogo_actionPerformed();
++    }
 +    else if (evt.getSource() == showConsensusHistogram)
 +    {
 +      showConsensusHistogram_actionPerformed();
 +    }
 +    else if (evt.getSource() == applyAutoAnnotationSettings)
 +    {
 +      applyAutoAnnotationSettings_actionPerformed();
 +    }
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  private void mouseOverFlag_stateChanged()
 +  {
 +    viewport.followHighlight = followMouseOverFlag.getState();
 +    // TODO: could kick the scrollTo mechanism to reset view for current
 +    // searchresults.
 +  }
 +
 +  private void centreColumnLabelFlag_stateChanged()
 +  {
 +    viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 +    this.alignPanel.annotationPanel.repaint();
 +  }
 +
 +  @Override
 +  public void actionPerformed(ActionEvent evt)
 +  {
 +    Object source = evt.getSource();
 +
 +    if (source == inputText)
 +    {
 +      inputText_actionPerformed();
 +    }
 +    else if (source == loadTree)
 +    {
 +      loadTree_actionPerformed();
 +    }
 +    else if (source == loadApplication)
 +    {
 +      launchFullApplication();
 +    }
 +    else if (source == loadAnnotations)
 +    {
 +      loadAnnotations();
 +    }
 +    else if (source == outputAnnotations)
 +    {
 +      outputAnnotations(true);
 +    }
 +    else if (source == outputFeatures)
 +    {
 +      outputFeatures(true, "Jalview");
 +    }
 +    else if (source == closeMenuItem)
 +    {
 +      closeMenuItem_actionPerformed();
 +    }
 +    else if (source == copy)
 +    {
 +      copy_actionPerformed();
 +    }
 +    else if (source == undoMenuItem)
 +    {
 +      undoMenuItem_actionPerformed();
 +    }
 +    else if (source == redoMenuItem)
 +    {
 +      redoMenuItem_actionPerformed();
 +    }
 +    else if (source == inputText)
 +    {
 +      inputText_actionPerformed();
 +    }
 +    else if (source == closeMenuItem)
 +    {
 +      closeMenuItem_actionPerformed();
 +    }
 +    else if (source == undoMenuItem)
 +    {
 +      undoMenuItem_actionPerformed();
 +    }
 +    else if (source == redoMenuItem)
 +    {
 +      redoMenuItem_actionPerformed();
 +    }
 +    else if (source == copy)
 +    {
 +      copy_actionPerformed();
 +    }
 +    else if (source == pasteNew)
 +    {
 +      pasteNew_actionPerformed();
 +    }
 +    else if (source == pasteThis)
 +    {
 +      pasteThis_actionPerformed();
 +    }
 +    else if (source == cut)
 +    {
 +      cut_actionPerformed();
 +    }
 +    else if (source == delete)
 +    {
 +      delete_actionPerformed();
 +    }
 +    else if (source == grpsFromSelection)
 +    {
 +      makeGrpsFromSelection_actionPerformed();
 +    }
 +    else if (source == deleteGroups)
 +    {
 +      deleteGroups_actionPerformed();
 +    }
 +    else if (source == selectAllSequenceMenuItem)
 +    {
 +      selectAllSequenceMenuItem_actionPerformed();
 +    }
 +    else if (source == deselectAllSequenceMenuItem)
 +    {
 +      deselectAllSequenceMenuItem_actionPerformed();
 +    }
 +    else if (source == invertSequenceMenuItem)
 +    {
 +      invertSequenceMenuItem_actionPerformed();
 +    }
 +    else if (source == invertColSel)
 +    {
 +      viewport.invertColumnSelection();
 +      alignPanel.paintAlignment(true);
 +    }
 +    else if (source == remove2LeftMenuItem)
 +    {
 +      trimAlignment(true);
 +    }
 +    else if (source == remove2RightMenuItem)
 +    {
 +      trimAlignment(false);
 +    }
 +    else if (source == removeGappedColumnMenuItem)
 +    {
 +      removeGappedColumnMenuItem_actionPerformed();
 +    }
 +    else if (source == removeAllGapsMenuItem)
 +    {
 +      removeAllGapsMenuItem_actionPerformed();
 +    }
 +    else if (source == findMenuItem)
 +    {
 +      findMenuItem_actionPerformed();
 +    }
 +    else if (source == font)
 +    {
 +      new FontChooser(alignPanel);
 +    }
 +    else if (source == newView)
 +    {
 +      newView(null);
 +    }
 +    else if (source == showColumns)
 +    {
 +      viewport.showAllHiddenColumns();
 +      alignPanel.paintAlignment(true);
 +    }
 +    else if (source == showSeqs)
 +    {
 +      viewport.showAllHiddenSeqs();
 +      alignPanel.paintAlignment(true);
 +    }
 +    else if (source == hideColumns)
 +    {
 +      viewport.hideSelectedColumns();
 +      alignPanel.paintAlignment(true);
 +    }
 +    else if (source == hideSequences
 +            && viewport.getSelectionGroup() != null)
 +    {
 +      viewport.hideAllSelectedSeqs();
 +      alignPanel.paintAlignment(true);
 +    }
 +    else if (source == hideAllButSelection)
 +    {
 +      toggleHiddenRegions(false, false);
 +      alignPanel.paintAlignment(true);
 +    }
 +    else if (source == hideAllSelection)
 +    {
 +      SequenceGroup sg = viewport.getSelectionGroup();
 +      viewport.expandColSelection(sg, false);
 +      viewport.hideAllSelectedSeqs();
 +      viewport.hideSelectedColumns();
 +      alignPanel.paintAlignment(true);
 +    }
 +    else if (source == showAllHidden)
 +    {
 +      viewport.showAllHiddenColumns();
 +      viewport.showAllHiddenSeqs();
 +      alignPanel.paintAlignment(true);
 +    }
 +    else if (source == showGroupConsensus)
 +    {
 +      showGroupConsensus_actionPerformed();
 +    }
 +    else if (source == showGroupConservation)
 +    {
 +      showGroupConservation_actionPerformed();
 +    }
 +    else if (source == showSequenceLogo)
 +    {
 +      showSequenceLogo_actionPerformed();
 +    }
++    else if (source == normSequenceLogo)
++    {
++      normSequenceLogo_actionPerformed();
++    }
 +    else if (source == showConsensusHistogram)
 +    {
 +      showConsensusHistogram_actionPerformed();
 +    }
 +    else if (source == applyAutoAnnotationSettings)
 +    {
 +      applyAutoAnnotationSettings_actionPerformed();
 +    }
 +    else if (source == featureSettings)
 +    {
 +      new FeatureSettings(alignPanel);
 +    }
 +    else if (source == alProperties)
 +    {
 +      StringBuffer contents = new jalview.io.AlignmentProperties(
 +              viewport.getAlignment()).formatAsString();
 +      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
 +      cap.setText(contents.toString());
 +      Frame frame = new Frame();
 +      frame.add(cap);
 +      jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
 +              + getTitle(), 400, 250);
 +    }
 +    else if (source == overviewMenuItem)
 +    {
 +      overviewMenuItem_actionPerformed();
 +    }
 +    else if (source == noColourmenuItem)
 +    {
 +      changeColour(null);
 +    }
 +    else if (source == clustalColour)
 +    {
 +      abovePIDThreshold.setState(false);
-       changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));
++      changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
 +    }
 +    else if (source == zappoColour)
 +    {
 +      changeColour(new ZappoColourScheme());
 +    }
 +    else if (source == taylorColour)
 +    {
 +      changeColour(new TaylorColourScheme());
 +    }
 +    else if (source == hydrophobicityColour)
 +    {
 +      changeColour(new HydrophobicColourScheme());
 +    }
 +    else if (source == helixColour)
 +    {
 +      changeColour(new HelixColourScheme());
 +    }
 +    else if (source == strandColour)
 +    {
 +      changeColour(new StrandColourScheme());
 +    }
 +    else if (source == turnColour)
 +    {
 +      changeColour(new TurnColourScheme());
 +    }
 +    else if (source == buriedColour)
 +    {
 +      changeColour(new BuriedColourScheme());
 +    }
 +    else if (source == nucleotideColour)
 +    {
 +      changeColour(new NucleotideColourScheme());
 +    }
 +    else if (source == purinePyrimidineColour)
 +    {
 +      changeColour(new PurinePyrimidineColourScheme());
 +    }
 +    else if (source == RNAInteractionColour)
 +    {
 +      changeColour(new RNAInteractionColourScheme());
 +    }
 +    else if (source == RNAHelixColour)
 +    {
 +      new RNAHelicesColourChooser(viewport, alignPanel);
 +    }
 +    else if (source == modifyPID)
 +    {
 +      modifyPID_actionPerformed();
 +    }
 +    else if (source == modifyConservation)
 +    {
 +      modifyConservation_actionPerformed();
 +    }
 +    else if (source == userDefinedColour)
 +    {
 +      new UserDefinedColours(alignPanel, null);
 +    }
 +    else if (source == PIDColour)
 +    {
 +      changeColour(new PIDColourScheme());
 +    }
 +    else if (source == BLOSUM62Colour)
 +    {
 +      changeColour(new Blosum62ColourScheme());
 +    }
-     else if (source == tcoffeeColour) {
-         changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
++    else if (source == tcoffeeColour)
++    {
++      changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
 +    }
 +    else if (source == annotationColour)
 +    {
 +      new AnnotationColourChooser(viewport, alignPanel);
 +    }
 +    else if (source == sortPairwiseMenuItem)
 +    {
 +      sortPairwiseMenuItem_actionPerformed();
 +    }
 +    else if (source == sortIDMenuItem)
 +    {
 +      sortIDMenuItem_actionPerformed();
 +    }
 +    else if (source == sortLengthMenuItem)
 +    {
 +      sortLengthMenuItem_actionPerformed();
 +    }
 +    else if (source == sortGroupMenuItem)
 +    {
 +      sortGroupMenuItem_actionPerformed();
 +    }
 +    else if (source == removeRedundancyMenuItem)
 +    {
 +      removeRedundancyMenuItem_actionPerformed();
 +    }
 +    else if (source == pairwiseAlignmentMenuItem)
 +    {
 +      pairwiseAlignmentMenuItem_actionPerformed();
 +    }
 +    else if (source == PCAMenuItem)
 +    {
 +      PCAMenuItem_actionPerformed();
 +    }
 +    else if (source == averageDistanceTreeMenuItem)
 +    {
 +      averageDistanceTreeMenuItem_actionPerformed();
 +    }
 +    else if (source == neighbourTreeMenuItem)
 +    {
 +      neighbourTreeMenuItem_actionPerformed();
 +    }
 +    else if (source == njTreeBlosumMenuItem)
 +    {
 +      njTreeBlosumMenuItem_actionPerformed();
 +    }
 +    else if (source == avDistanceTreeBlosumMenuItem)
 +    {
 +      avTreeBlosumMenuItem_actionPerformed();
 +    }
 +    else if (source == documentation)
 +    {
 +      documentation_actionPerformed();
 +    }
 +    else if (source == about)
 +    {
 +      about_actionPerformed();
 +    }
 +
 +  }
 +
 +  public void inputText_actionPerformed()
 +  {
 +    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
 +    Frame frame = new Frame();
 +    frame.add(cap);
 +    jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
 +  }
 +
 +  protected void outputText_actionPerformed(ActionEvent e)
 +  {
 +    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
 +    Frame frame = new Frame();
 +    frame.add(cap);
 +    jalview.bin.JalviewLite.addFrame(frame,
 +            "Alignment output - " + e.getActionCommand(), 600, 500);
 +    cap.setText(new AppletFormatAdapter().formatSequences(
 +            e.getActionCommand(), viewport.getAlignment(),
 +            viewport.showJVSuffix));
 +  }
 +
 +  public void loadAnnotations()
 +  {
 +    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
 +    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.getAlignment()
-                     .getAlignmentAnnotation() : null, viewport.getAlignment()
-                     .getGroups(),
-             ((Alignment) viewport.getAlignment()).alignmentProperties);
++                    .getAlignmentAnnotation() : null, viewport
++                    .getAlignment().getGroups(), ((Alignment) viewport
++                    .getAlignment()).alignmentProperties);
 +
 +    if (displayTextbox)
 +    {
 +      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
 +      Frame frame = new Frame();
 +      frame.add(cap);
 +      jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
 +      cap.setText(annotation);
 +    }
 +
 +    return annotation;
 +  }
 +
 +  private Hashtable getDisplayedFeatureCols()
 +  {
-     if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
++    if (alignPanel.getFeatureRenderer() != null
++            && viewport.featuresDisplayed != null)
 +    {
 +      FeatureRenderer fr = alignPanel.getFeatureRenderer();
 +      Hashtable fcols = new Hashtable();
 +      Enumeration en = viewport.featuresDisplayed.keys();
 +      while (en.hasMoreElements())
 +      {
 +        Object col = en.nextElement();
 +        fcols.put(col, fr.featureColours.get(col));
 +      }
 +      return fcols;
 +    }
 +    return null;
 +  }
 +
 +  public String outputFeatures(boolean displayTextbox, String format)
 +  {
 +    String features;
 +    if (format.equalsIgnoreCase("Jalview"))
 +    {
-       features = new FeaturesFile().printJalviewFormat(
-               viewport.getAlignment().getSequencesArray(),
++      features = new FeaturesFile().printJalviewFormat(viewport
++              .getAlignment().getSequencesArray(),
 +              getDisplayedFeatureCols());
 +    }
 +    else
 +    {
-       features = new FeaturesFile().printGFFFormat(
-               viewport.getAlignment().getSequencesArray(),
-               getDisplayedFeatureCols());
++      features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
++              .getSequencesArray(), getDisplayedFeatureCols());
 +    }
 +
 +    if (displayTextbox)
 +    {
-       boolean frimport=false;
-       if (features==null || features.equals("No Features Visible"))
++      boolean frimport = false;
++      if (features == null || features.equals("No Features Visible"))
 +      {
 +        features = "# No features visible - paste some and import them here.";
-         frimport=true;
++        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)
++    }
++    else
++    {
++      if (features == null)
 +        features = "";
 +    }
 +
 +    return features;
 +  }
 +
 +  void launchFullApplication()
 +  {
 +    StringBuffer url = new StringBuffer(jalviewServletURL);
 +
 +    url.append("?open="
 +            + appendProtocol(viewport.applet.getParameter("file")));
 +
 +    if (viewport.applet.getParameter("features") != null)
 +    {
 +      url.append("&features=");
 +      url.append(appendProtocol(viewport.applet.getParameter("features")));
 +    }
 +
 +    if (viewport.applet.getParameter("annotations") != null)
 +    {
 +      url.append("&annotations=");
 +      url.append(appendProtocol(viewport.applet.getParameter("annotations")));
 +    }
 +
 +    if (viewport.applet.getParameter("jnetfile") != null)
 +    {
 +      url.append("&annotations=");
 +      url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
 +    }
 +
 +    if (viewport.applet.getParameter("defaultColour") != null)
 +    {
 +      url.append("&colour="
 +              + removeWhiteSpace(viewport.applet
 +                      .getParameter("defaultColour")));
 +    }
 +
 +    if (viewport.applet.getParameter("userDefinedColour") != null)
 +    {
 +      url.append("&colour="
 +              + removeWhiteSpace(viewport.applet
 +                      .getParameter("userDefinedColour")));
 +    }
 +    if (viewport.applet.getParameter("tree") != null)
 +    {
 +      url.append("&tree="
 +              + appendProtocol(viewport.applet.getParameter("tree")));
 +    }
 +    if (viewport.applet.getParameter("treeFile") != null)
 +    {
 +      url.append("&tree="
 +              + appendProtocol(viewport.applet.getParameter("treeFile")));
 +    }
 +
 +    showURL(url.toString(), "FULL_APP");
 +  }
 +
 +  String removeWhiteSpace(String colour)
 +  {
 +    StringBuffer sb = new StringBuffer();
 +    for (int i = 0; i < colour.length(); i++)
 +    {
 +      if (Character.isWhitespace(colour.charAt(i)))
 +      {
 +        sb.append("%20");
 +      }
 +      else
 +      {
 +        sb.append(colour.charAt(i));
 +      }
 +    }
 +
 +    return sb.toString();
 +  }
 +
 +  String appendProtocol(String url)
 +  {
 +    try
 +    {
 +      new URL(url);
 +      url = URLEncoder.encode(url);
 +    }
 +    /*
 +     * When we finally deprecate 1.1 compatibility, we can start to use
 +     * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
 +     * (UnsupportedEncodingException ex) { System.err.println("WARNING -
 +     * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
 +     * ex.printStackTrace(); }
 +     */
 +    catch (java.net.MalformedURLException ex)
 +    {
 +      url = viewport.applet.getCodeBase() + url;
 +    }
 +    return url;
 +  }
 +
 +  public void closeMenuItem_actionPerformed()
 +  {
 +    PaintRefresher.RemoveComponent(alignPanel);
-     if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)
++    if (alignPanel.seqPanel != null
++            && alignPanel.seqPanel.seqCanvas != null)
 +    {
 +      PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
 +    }
-     if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {
++    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 {
++    }
++    else
++    {
 +    }
 +    viewport = null;
 +    alignPanel = null;
 +    this.dispose();
 +  }
 +
 +  /**
 +   * TODO: JAL-1104
 +   */
 +  void updateEditMenuBar()
 +  {
 +
 +    if (viewport.historyList.size() > 0)
 +    {
 +      undoMenuItem.setEnabled(true);
 +      CommandI command = (CommandI) viewport.historyList.peek();
 +      undoMenuItem.setLabel("Undo " + command.getDescription());
 +    }
 +    else
 +    {
 +      undoMenuItem.setEnabled(false);
 +      undoMenuItem.setLabel("Undo");
 +    }
 +
 +    if (viewport.redoList.size() > 0)
 +    {
 +      redoMenuItem.setEnabled(true);
 +
 +      CommandI command = (CommandI) viewport.redoList.peek();
 +      redoMenuItem.setLabel("Redo " + command.getDescription());
 +    }
 +    else
 +    {
 +      redoMenuItem.setEnabled(false);
 +      redoMenuItem.setLabel("Redo");
 +    }
 +  }
 +
 +  /**
 +   * TODO: JAL-1104
 +   */
 +  public void addHistoryItem(CommandI command)
 +  {
 +    if (command.getSize() > 0)
 +    {
 +      viewport.historyList.push(command);
 +      viewport.redoList.removeAllElements();
 +      updateEditMenuBar();
 +      viewport.updateHiddenColumns();
 +    }
 +  }
 +
 +  /**
-    * TODO: JAL-1104
-    * DOCUMENT ME!
-    *
++   * TODO: JAL-1104 DOCUMENT ME!
++   * 
 +   * @param e
 +   *          DOCUMENT ME!
 +   */
 +  protected void undoMenuItem_actionPerformed()
 +  {
 +    if (viewport.historyList.size() < 1)
 +    {
 +      return;
 +    }
 +
 +    CommandI command = (CommandI) viewport.historyList.pop();
 +    viewport.redoList.push(command);
 +    command.undoCommand(null);
 +
 +    AlignViewport originalSource = getOriginatingSource(command);
 +    // JBPNote Test
-     if (originalSource!=viewport) {
-       System.err.println("Warning: Viewport object mismatch whilst undoing");
++    if (originalSource != viewport)
++    {
++      System.err
++              .println("Warning: Viewport object mismatch whilst undoing");
 +    }
-     originalSource.updateHiddenColumns(); //    originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
++    originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
++                                          // viewport.getColumnSelection().getHiddenColumns()
++                                          // != null;
 +    updateEditMenuBar();
-     originalSource.firePropertyChange("alignment", null,
-             originalSource.getAlignment().getSequences());
++    originalSource.firePropertyChange("alignment", null, originalSource
++            .getAlignment().getSequences());
 +  }
 +
 +  /**
-    * TODO: JAL-1104
-    * DOCUMENT ME!
-    *
++   * TODO: JAL-1104 DOCUMENT ME!
++   * 
 +   * @param e
 +   *          DOCUMENT ME!
 +   */
 +  protected void redoMenuItem_actionPerformed()
 +  {
 +    if (viewport.redoList.size() < 1)
 +    {
 +      return;
 +    }
 +
 +    CommandI command = (CommandI) viewport.redoList.pop();
 +    viewport.historyList.push(command);
 +    command.doCommand(null);
 +
 +    AlignViewport originalSource = getOriginatingSource(command);
 +    // JBPNote Test
-     if (originalSource!=viewport) {
-       System.err.println("Warning: Viewport object mismatch whilst re-doing");
++    if (originalSource != viewport)
++    {
++      System.err
++              .println("Warning: Viewport object mismatch whilst re-doing");
 +    }
-     originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
++    originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
++                                          // viewport.getColumnSelection().getHiddenColumns()
++                                          // != null;
 +
 +    updateEditMenuBar();
-     originalSource.firePropertyChange("alignment", null,
-             originalSource.getAlignment().getSequences());
++    originalSource.firePropertyChange("alignment", null, originalSource
++            .getAlignment().getSequences());
 +  }
 +
 +  AlignViewport getOriginatingSource(CommandI command)
 +  {
 +    AlignViewport originalSource = null;
 +    // For sequence removal and addition, we need to fire
 +    // the property change event FROM the viewport where the
 +    // original alignment was altered
 +    AlignmentI al = null;
 +    if (command instanceof EditCommand)
 +    {
 +      EditCommand editCommand = (EditCommand) command;
 +      al = editCommand.getAlignment();
 +      Vector comps = (Vector) PaintRefresher.components.get(viewport
 +              .getSequenceSetId());
 +      for (int i = 0; i < comps.size(); i++)
 +      {
 +        if (comps.elementAt(i) instanceof AlignmentPanel)
 +        {
 +          if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
 +          {
 +            originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
 +            break;
 +          }
 +        }
 +      }
 +    }
 +
 +    if (originalSource == null)
 +    {
 +      // The original view is closed, we must validate
 +      // the current view against the closed view first
 +      if (al != null)
 +      {
 +        PaintRefresher.validateSequences(al, viewport.getAlignment());
 +      }
 +
 +      originalSource = viewport;
 +    }
 +
 +    return originalSource;
 +  }
 +
 +  public void moveSelectedSequences(boolean up)
 +  {
 +    SequenceGroup sg = viewport.getSelectionGroup();
 +    if (sg == null)
 +    {
 +      return;
 +    }
-     viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);
++    viewport.getAlignment().moveSelectedSequencesByOne(sg,
++            up ? null : viewport.getHiddenRepSequences(), up);
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  synchronized void slideSequences(boolean right, int size)
 +  {
-     List<SequenceI>sg = new Vector<SequenceI>();
++    List<SequenceI> sg = new Vector<SequenceI>();
 +    if (viewport.cursorMode)
 +    {
-       sg.add(viewport.getAlignment()
-               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
++      sg.add(viewport.getAlignment().getSequenceAt(
++              alignPanel.seqPanel.seqCanvas.cursorY));
 +    }
 +    else if (viewport.getSelectionGroup() != null
-             && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
-                     .getHeight())
++            && viewport.getSelectionGroup().getSize() != viewport
++                    .getAlignment().getHeight())
 +    {
 +      sg = viewport.getSelectionGroup().getSequences(
 +              viewport.getHiddenRepSequences());
 +    }
 +
 +    if (sg.size() < 1)
 +    {
 +      return;
 +    }
 +
 +    Vector<SequenceI> invertGroup = new Vector();
 +
 +    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
 +    {
 +      if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
 +        invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
 +    }
 +
 +    SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
 +
-     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);
++    SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
++            .size()]);
 +    for (int i = 0; i < invertGroup.size(); i++)
 +      seqs2[i] = invertGroup.elementAt(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);
 +      else
 +        groupAdjustment = size;
 +    }
 +    else if (!ssc.getGapsInsertedBegin() && !right)
 +    {
 +      if (viewport.cursorMode)
 +        alignPanel.seqPanel.moveCursor(-size, 0);
 +      else
 +        groupAdjustment = -size;
 +    }
 +
 +    if (groupAdjustment != 0)
 +    {
 +      viewport.getSelectionGroup().setStartRes(
 +              viewport.getSelectionGroup().getStartRes() + groupAdjustment);
 +      viewport.getSelectionGroup().setEndRes(
 +              viewport.getSelectionGroup().getEndRes() + groupAdjustment);
 +    }
 +
 +    boolean appendHistoryItem = false;
 +    if (viewport.historyList != null && viewport.historyList.size() > 0
 +            && viewport.historyList.peek() instanceof SlideSequencesCommand)
 +    {
 +      appendHistoryItem = ssc
 +              .appendSlideCommand((SlideSequencesCommand) viewport.historyList
 +                      .peek());
 +    }
 +
 +    if (!appendHistoryItem)
 +      addHistoryItem(ssc);
 +
 +    repaint();
 +  }
 +
 +  static StringBuffer copiedSequences;
 +
 +  static Vector copiedHiddenColumns;
 +
 +  protected void copy_actionPerformed()
 +  {
 +    if (viewport.getSelectionGroup() == null)
 +    {
 +      return;
 +    }
 +
 +    SequenceGroup sg = viewport.getSelectionGroup();
 +    copiedSequences = new StringBuffer();
 +    Hashtable orderedSeqs = new Hashtable();
 +    for (int i = 0; i < sg.getSize(); i++)
 +    {
 +      SequenceI seq = sg.getSequenceAt(i);
 +      int index = viewport.getAlignment().findIndex(seq);
 +      orderedSeqs.put(index + "", seq);
 +    }
 +
 +    int index = 0, startRes, endRes;
 +    char ch;
 +
 +    if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
 +    {
 +      copiedHiddenColumns = new Vector();
 +      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
 +      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
 +              .size(); i++)
 +      {
 +        int[] region = (int[]) viewport.getColumnSelection()
 +                .getHiddenColumns().elementAt(i);
 +
 +        copiedHiddenColumns.addElement(new int[]
 +        { region[0] - hiddenOffset, region[1] - hiddenOffset });
 +      }
 +    }
 +    else
 +    {
 +      copiedHiddenColumns = null;
 +    }
 +
 +    for (int i = 0; i < sg.getSize(); i++)
 +    {
 +      SequenceI seq = null;
 +
 +      while (seq == null)
 +      {
 +        if (orderedSeqs.containsKey(index + ""))
 +        {
 +          seq = (SequenceI) orderedSeqs.get(index + "");
 +          index++;
 +
 +          break;
 +        }
 +        else
 +        {
 +          index++;
 +        }
 +      }
 +
 +      // FIND START RES
 +      // Returns residue following index if gap
 +      startRes = seq.findPosition(sg.getStartRes());
 +
 +      // FIND END RES
 +      // Need to find the residue preceeding index if gap
 +      endRes = 0;
 +
 +      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
 +      {
 +        ch = seq.getCharAt(j);
 +        if (!jalview.util.Comparison.isGap((ch)))
 +        {
 +          endRes++;
 +        }
 +      }
 +
 +      if (endRes > 0)
 +      {
 +        endRes += seq.getStart() - 1;
 +      }
 +
 +      copiedSequences.append(seq.getName()
 +              + "\t"
 +              + startRes
 +              + "\t"
 +              + endRes
 +              + "\t"
 +              + seq.getSequenceAsString(sg.getStartRes(),
 +                      sg.getEndRes() + 1) + "\n");
 +    }
 +
 +  }
 +
 +  protected void pasteNew_actionPerformed()
 +  {
 +    paste(true);
 +  }
 +
 +  protected void pasteThis_actionPerformed()
 +  {
 +    paste(false);
 +  }
 +
 +  void paste(boolean newAlignment)
 +  {
 +    try
 +    {
 +
 +      if (copiedSequences == null)
 +      {
 +        return;
 +      }
 +
 +      StringTokenizer st = new StringTokenizer(copiedSequences.toString());
 +      Vector seqs = new Vector();
 +      while (st.hasMoreElements())
 +      {
 +        String name = st.nextToken();
 +        int start = Integer.parseInt(st.nextToken());
 +        int end = Integer.parseInt(st.nextToken());
 +        seqs.addElement(new Sequence(name, st.nextToken(), start, end));
 +      }
 +      SequenceI[] newSeqs = new SequenceI[seqs.size()];
 +      for (int i = 0; i < seqs.size(); i++)
 +      {
 +        newSeqs[i] = (SequenceI) seqs.elementAt(i);
 +      }
 +
 +      if (newAlignment)
 +      {
 +        String newtitle = new String("Copied sequences");
 +        if (getTitle().startsWith("Copied sequences"))
 +        {
 +          newtitle = getTitle();
 +        }
 +        else
 +        {
 +          newtitle = newtitle.concat("- from " + getTitle());
 +        }
 +        AlignFrame af = new AlignFrame(new Alignment(newSeqs),
 +                viewport.applet, newtitle, false);
 +        if (copiedHiddenColumns != null)
 +        {
 +          for (int i = 0; i < copiedHiddenColumns.size(); i++)
 +          {
 +            int[] region = (int[]) copiedHiddenColumns.elementAt(i);
 +            af.viewport.hideColumns(region[0], region[1]);
 +          }
 +        }
 +
 +        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
 +                DEFAULT_HEIGHT);
 +      }
 +      else
 +      {
 +        addSequences(newSeqs);
 +      }
 +
 +    } catch (Exception ex)
 +    {
 +    } // could be anything being pasted in here
 +
 +  }
 +
 +  void addSequences(SequenceI[] seqs)
 +  {
 +    for (int i = 0; i < seqs.length; i++)
 +    {
 +      viewport.getAlignment().addSequence(seqs[i]);
 +    }
 +
 +    // !newAlignment
 +    addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
-             seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
++            seqs, 0, viewport.getAlignment().getWidth(),
++            viewport.getAlignment()));
 +
 +    viewport.setEndSeq(viewport.getAlignment().getHeight());
 +    viewport.getAlignment().getWidth();
-     viewport.firePropertyChange("alignment", null,
-             viewport.getAlignment().getSequences());
++    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
++            .getSequences());
 +
 +  }
 +
 +  protected void cut_actionPerformed()
 +  {
 +    copy_actionPerformed();
 +    delete_actionPerformed();
 +  }
 +
 +  protected void delete_actionPerformed()
 +  {
 +
 +    SequenceGroup sg = viewport.getSelectionGroup();
 +    if (sg == null)
 +    {
 +      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 (sg.getSize() == viewport.getAlignment().getHeight())
 +    {
 +      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);
 +    }
 +
 +    /*
 +     * //ADD HISTORY ITEM
 +     */
 +    addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
 +            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
 +            viewport.getAlignment()));
 +
 +    viewport.setSelectionGroup(null);
 +    viewport.getAlignment().deleteGroup(sg);
 +
 +    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
 +            .getSequences());
 +
 +    if (viewport.getAlignment().getHeight() < 1)
 +    {
 +      this.setVisible(false);
 +    }
 +    viewport.sendSelection();
 +  }
 +
 +  /**
 +   * group consensus toggled
-    *
++   * 
 +   */
 +  protected void showGroupConsensus_actionPerformed()
 +  {
 +    viewport.setShowGroupConsensus(showGroupConsensus.getState());
 +    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 +
 +  }
 +
 +  /**
 +   * group conservation toggled.
 +   */
 +  protected void showGroupConservation_actionPerformed()
 +  {
 +    viewport.setShowGroupConservation(showGroupConservation.getState());
 +    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 +  }
 +
 +  /*
 +   * (non-Javadoc)
-    *
++   * 
 +   * @see
 +   * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
 +   * .event.ActionEvent)
 +   */
 +  protected void showConsensusHistogram_actionPerformed()
 +  {
 +    viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
 +    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 +  }
++
 +  /*
 +   * (non-Javadoc)
-    *
++   * 
 +   * @see
 +   * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
 +   * .event.ActionEvent)
 +   */
 +  protected void showSequenceLogo_actionPerformed()
 +  {
 +    viewport.setShowSequenceLogo(showSequenceLogo.getState());
 +    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 +  }
 +
++  protected void normSequenceLogo_actionPerformed()
++  {
++    showSequenceLogo.setState(true);
++    viewport.setShowSequenceLogo(true);
++    viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
++    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
++  }
++
 +  protected void applyAutoAnnotationSettings_actionPerformed()
 +  {
 +    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 +  }
 +
 +  protected void makeGrpsFromSelection_actionPerformed()
 +  {
 +    if (viewport.getSelectionGroup() != null)
 +    {
 +      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
 +              viewport.getSequenceSelection(),
 +              viewport.getAlignmentView(true).getSequenceStrings(
-                       viewport.getGapCharacter()),
-               viewport.getAlignment().getGroups());
++                      viewport.getGapCharacter()), viewport.getAlignment()
++                      .getGroups());
 +      viewport.getAlignment().deleteAllGroups();
 +      viewport.sequenceColours = null;
 +      viewport.setSelectionGroup(null);
 +      // set view properties for each group
 +      for (int g = 0; g < gps.length; g++)
 +      {
 +        // gps[g].setShowunconserved(viewport.getShowUnconserved());
 +        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
 +        viewport.getAlignment().addGroup(gps[g]);
 +        Color col = new Color((int) (Math.random() * 255),
 +                (int) (Math.random() * 255), (int) (Math.random() * 255));
 +        col = col.brighter();
 +        for (SequenceI sq : gps[g].getSequences(null))
-           viewport.setSequenceColour(
-                 sq, col)
-           ;
++          viewport.setSequenceColour(sq, col);
 +      }
 +      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
 +      alignPanel.updateAnnotation();
 +      alignPanel.paintAlignment(true);
 +    }
 +  }
 +
 +  protected void deleteGroups_actionPerformed()
 +  {
 +    viewport.getAlignment().deleteAllGroups();
 +    viewport.sequenceColours = null;
 +    viewport.setSelectionGroup(null);
 +
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  public void selectAllSequenceMenuItem_actionPerformed()
 +  {
 +    SequenceGroup sg = new SequenceGroup();
 +    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 +    {
 +      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
 +    }
 +    sg.setEndRes(viewport.getAlignment().getWidth() - 1);
 +    viewport.setSelectionGroup(sg);
 +    alignPanel.paintAlignment(true);
 +    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
 +    viewport.sendSelection();
 +  }
 +
 +  public void deselectAllSequenceMenuItem_actionPerformed()
 +  {
 +    if (viewport.cursorMode)
 +    {
 +      alignPanel.seqPanel.keyboardNo1 = null;
 +      alignPanel.seqPanel.keyboardNo2 = null;
 +    }
 +    viewport.setSelectionGroup(null);
 +    viewport.getColumnSelection().clear();
 +    viewport.setSelectionGroup(null);
 +    alignPanel.idPanel.idCanvas.searchResults = null;
 +    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
 +    alignPanel.paintAlignment(true);
 +    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
 +    viewport.sendSelection();
 +  }
 +
 +  public void invertSequenceMenuItem_actionPerformed()
 +  {
 +    SequenceGroup sg = viewport.getSelectionGroup();
 +    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 +    {
 +      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
 +    }
 +
 +    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
 +    viewport.sendSelection();
 +  }
 +
 +  public void invertColSel_actionPerformed()
 +  {
 +    viewport.invertColumnSelection();
 +    alignPanel.paintAlignment(true);
 +    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
 +    viewport.sendSelection();
 +  }
 +
 +  void trimAlignment(boolean trimLeft)
 +  {
 +    ColumnSelection colSel = viewport.getColumnSelection();
 +    int column;
 +
 +    if (colSel.size() > 0)
 +    {
 +      if (trimLeft)
 +      {
 +        column = colSel.getMin();
 +      }
 +      else
 +      {
 +        column = colSel.getMax();
 +      }
 +
 +      SequenceI[] seqs;
 +      if (viewport.getSelectionGroup() != null)
 +      {
 +        seqs = viewport.getSelectionGroup().getSequencesAsArray(
 +                viewport.getHiddenRepSequences());
 +      }
 +      else
 +      {
 +        seqs = viewport.getAlignment().getSequencesArray();
 +      }
 +
 +      TrimRegionCommand trimRegion;
 +      if (trimLeft)
 +      {
 +        trimRegion = new TrimRegionCommand("Remove Left",
 +                TrimRegionCommand.TRIM_LEFT, seqs, column,
 +                viewport.getAlignment(), viewport.getColumnSelection(),
 +                viewport.getSelectionGroup());
 +        viewport.setStartRes(0);
 +      }
 +      else
 +      {
 +        trimRegion = new TrimRegionCommand("Remove Right",
 +                TrimRegionCommand.TRIM_RIGHT, seqs, column,
 +                viewport.getAlignment(), viewport.getColumnSelection(),
 +                viewport.getSelectionGroup());
 +      }
 +
 +      statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
 +
 +      addHistoryItem(trimRegion);
 +
- 
- 
-       for (SequenceGroup sg:viewport.getAlignment().getGroups())
++      for (SequenceGroup sg : viewport.getAlignment().getGroups())
 +      {
 +        if ((trimLeft && !sg.adjustForRemoveLeft(column))
 +                || (!trimLeft && !sg.adjustForRemoveRight(column)))
 +        {
 +          viewport.getAlignment().deleteGroup(sg);
 +        }
 +      }
 +
 +      viewport.firePropertyChange("alignment", null, viewport
 +              .getAlignment().getSequences());
 +    }
 +  }
 +
 +  public void removeGappedColumnMenuItem_actionPerformed()
 +  {
 +    int start = 0, end = viewport.getAlignment().getWidth() - 1;
 +
 +    SequenceI[] seqs;
 +    if (viewport.getSelectionGroup() != null)
 +    {
 +      seqs = viewport.getSelectionGroup().getSequencesAsArray(
 +              viewport.getHiddenRepSequences());
 +      start = viewport.getSelectionGroup().getStartRes();
 +      end = viewport.getSelectionGroup().getEndRes();
 +    }
 +    else
 +    {
 +      seqs = viewport.getAlignment().getSequencesArray();
 +    }
 +
 +    RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
-             "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
++            "Remove Gapped Columns", seqs, start, end,
++            viewport.getAlignment());
 +
 +    addHistoryItem(removeGapCols);
 +
 +    statusBar.setText("Removed " + removeGapCols.getSize()
 +            + " empty columns.");
 +
 +    // This is to maintain viewport position on first residue
 +    // of first sequence
 +    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
 +    int startRes = seq.findPosition(viewport.startRes);
 +    // ShiftList shifts;
 +    // viewport.getAlignment().removeGaps(shifts=new ShiftList());
 +    // edit.alColumnChanges=shifts.getInverse();
 +    // if (viewport.hasHiddenColumns)
 +    // viewport.getColumnSelection().compensateForEdits(shifts);
 +    viewport.setStartRes(seq.findIndex(startRes) - 1);
 +    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
 +            .getSequences());
 +
 +  }
 +
 +  public void removeAllGapsMenuItem_actionPerformed()
 +  {
 +    int start = 0, end = viewport.getAlignment().getWidth() - 1;
 +
 +    SequenceI[] seqs;
 +    if (viewport.getSelectionGroup() != null)
 +    {
 +      seqs = viewport.getSelectionGroup().getSequencesAsArray(
 +              viewport.getHiddenRepSequences());
 +      start = viewport.getSelectionGroup().getStartRes();
 +      end = viewport.getSelectionGroup().getEndRes();
 +    }
 +    else
 +    {
 +      seqs = viewport.getAlignment().getSequencesArray();
 +    }
 +
 +    // This is to maintain viewport position on first residue
 +    // of first sequence
 +    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
 +    int startRes = seq.findPosition(viewport.startRes);
 +
 +    addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
 +            viewport.getAlignment()));
 +
 +    viewport.setStartRes(seq.findIndex(startRes) - 1);
 +
 +    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
 +            .getSequences());
 +
 +  }
 +
 +  public void findMenuItem_actionPerformed()
 +  {
 +    new Finder(alignPanel);
 +  }
 +
 +  /**
 +   * create a new view derived from the current view
-    *
++   * 
 +   * @param viewtitle
 +   * @return frame for the new view
 +   */
 +  public AlignFrame newView(String viewtitle)
 +  {
 +    AlignmentI newal;
 +    if (viewport.hasHiddenRows())
 +    {
 +      newal = new Alignment(viewport.getAlignment().getHiddenSequences()
 +              .getFullAlignment().getSequencesArray());
 +    }
 +    else
 +    {
 +      newal = new Alignment(viewport.getAlignment().getSequencesArray());
 +    }
 +
 +    if (viewport.getAlignment().getAlignmentAnnotation() != null)
 +    {
 +      for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
 +      {
 +        if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
 +        {
-           newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
++          newal.addAnnotation(viewport.getAlignment()
++                  .getAlignmentAnnotation()[i]);
 +        }
 +      }
 +    }
 +
 +    AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
 +
 +    newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
 +    PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
 +    PaintRefresher.Register(newaf.alignPanel,
 +            newaf.alignPanel.av.getSequenceSetId());
 +
 +    PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
 +            newaf.alignPanel.av.getSequenceSetId());
 +    PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
 +            newaf.alignPanel.av.getSequenceSetId());
 +
 +    Vector comps = (Vector) PaintRefresher.components.get(viewport
 +            .getSequenceSetId());
 +    int viewSize = -1;
 +    for (int i = 0; i < comps.size(); i++)
 +    {
 +      if (comps.elementAt(i) instanceof AlignmentPanel)
 +      {
 +        viewSize++;
 +      }
 +    }
 +
 +    String title = new String(this.getTitle());
 +    if (viewtitle != null)
 +    {
 +      title = viewtitle + " ( " + title + ")";
 +    }
 +    else
 +    {
 +      if (title.indexOf("(View") > -1)
 +      {
 +        title = title.substring(0, title.indexOf("(View"));
 +      }
 +      title += "(View " + viewSize + ")";
 +    }
 +
 +    newaf.setTitle(title.toString());
 +
 +    newaf.viewport.historyList = viewport.historyList;
 +    newaf.viewport.redoList = viewport.redoList;
 +    return newaf;
 +  }
 +
 +  /**
-    *
++   * 
 +   * @return list of feature groups on the view
 +   */
 +  public String[] getFeatureGroups()
 +  {
 +    FeatureRenderer fr = null;
 +    if (alignPanel != null
 +            && (fr = alignPanel.getFeatureRenderer()) != null)
 +    {
 +      return fr.getGroups();
 +    }
 +    return null;
 +  }
 +
 +  /**
 +   * get sequence feature groups that are hidden or shown
-    *
++   * 
 +   * @param visible
 +   *          true is visible
 +   * @return list
 +   */
 +  public String[] getFeatureGroupsOfState(boolean visible)
 +  {
 +    FeatureRenderer fr = null;
 +    if (alignPanel != null
 +            && (fr = alignPanel.getFeatureRenderer()) != null)
 +    {
 +      return fr.getGroups(visible);
 +    }
 +    return null;
 +  }
 +
 +  /**
 +   * Change the display state for the given feature groups
-    *
++   * 
 +   * @param groups
 +   *          list of group strings
 +   * @param state
 +   *          visible or invisible
 +   */
 +  public void setFeatureGroupState(String[] groups, boolean state)
 +  {
 +    FeatureRenderer fr = null;
 +    this.sequenceFeatures.setState(true);
 +    viewport.showSequenceFeatures(true);
 +    if (alignPanel != null
 +            && (fr = alignPanel.getFeatureRenderer()) != null)
 +    {
 +      fr.setGroupState(groups, state);
 +      alignPanel.seqPanel.seqCanvas.repaint();
 +      if (alignPanel.overviewPanel != null)
 +      {
 +        alignPanel.overviewPanel.updateOverviewImage();
 +      }
 +    }
 +  }
 +
 +  public void seqLimits_itemStateChanged()
 +  {
 +    viewport.setShowJVSuffix(seqLimits.getState());
 +    alignPanel.fontChanged();
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  protected void colourTextMenuItem_actionPerformed()
 +  {
 +    viewport.setColourText(colourTextMenuItem.getState());
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  protected void displayNonconservedMenuItem_actionPerformed()
 +  {
 +    viewport.setShowunconserved(displayNonconservedMenuItem.getState());
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  protected void wrapMenuItem_actionPerformed()
 +  {
 +    viewport.setWrapAlignment(wrapMenuItem.getState());
 +    alignPanel.setWrapAlignment(wrapMenuItem.getState());
 +    scaleAbove.setEnabled(wrapMenuItem.getState());
 +    scaleLeft.setEnabled(wrapMenuItem.getState());
 +    scaleRight.setEnabled(wrapMenuItem.getState());
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  public void overviewMenuItem_actionPerformed()
 +  {
 +    if (alignPanel.overviewPanel != null)
 +    {
 +      return;
 +    }
 +
 +    Frame frame = new Frame();
 +    OverviewPanel overview = new OverviewPanel(alignPanel);
 +    frame.add(overview);
 +    // +50 must allow for applet frame window
 +    jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
 +            overview.getPreferredSize().width,
 +            overview.getPreferredSize().height + 50);
 +
 +    frame.pack();
-     final AlignmentPanel ap=alignPanel;
++    final AlignmentPanel ap = alignPanel;
 +    frame.addWindowListener(new WindowAdapter()
 +    {
 +      @Override
 +      public void windowClosing(WindowEvent e)
 +      {
-         if (ap!=null) {
++        if (ap != null)
++        {
 +          ap.setOverviewPanel(null);
 +        }
 +      };
 +    });
 +
 +    alignPanel.setOverviewPanel(overview);
 +
 +  }
 +
 +  void changeColour(ColourSchemeI cs)
 +  {
 +    int threshold = 0;
 +
 +    if (cs != null)
 +    {
 +      if (viewport.getAbovePIDThreshold())
 +      {
 +        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
 +                "Background");
 +
 +        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 +
 +        viewport.setGlobalColourScheme(cs);
 +      }
 +      else
 +      {
 +        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
 +      }
 +
 +      if (viewport.getConservationSelected())
 +      {
 +
 +        Alignment al = (Alignment) viewport.getAlignment();
 +        Conservation c = new Conservation("All",
 +                ResidueProperties.propHash, 3, al.getSequences(), 0,
 +                al.getWidth() - 1);
 +
 +        c.calculate();
 +        c.verdict(false, viewport.getConsPercGaps());
 +
 +        cs.setConservation(c);
 +
 +        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
 +                cs, "Background"));
 +
 +      }
 +      else
 +      {
 +        cs.setConservation(null);
 +      }
 +
 +      cs.setConsensus(viewport.getSequenceConsensusHash());
 +
 +    }
 +    viewport.setGlobalColourScheme(cs);
 +
- 
 +    if (alignPanel.getOverviewPanel() != null)
 +    {
 +      alignPanel.getOverviewPanel().updateOverviewImage();
 +    }
 +
 +    jalview.structure.StructureSelectionManager
-             .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
-                     alignPanel);
++            .getStructureSelectionManager(viewport.applet)
++            .sequenceColoursChanged(alignPanel);
 +
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  protected void modifyPID_actionPerformed()
 +  {
 +    if (viewport.getAbovePIDThreshold()
 +            && viewport.getGlobalColourScheme() != null)
 +    {
 +      SliderPanel.setPIDSliderSource(alignPanel,
 +              viewport.getGlobalColourScheme(), "Background");
 +      SliderPanel.showPIDSlider();
 +    }
 +  }
 +
 +  protected void modifyConservation_actionPerformed()
 +  {
 +    if (viewport.getConservationSelected()
 +            && viewport.getGlobalColourScheme() != null)
 +    {
 +      SliderPanel.setConservationSlider(alignPanel,
 +              viewport.getGlobalColourScheme(), "Background");
 +      SliderPanel.showConservationSlider();
 +    }
 +  }
 +
 +  protected void conservationMenuItem_actionPerformed()
 +  {
 +    viewport.setConservationSelected(conservationMenuItem.getState());
 +
 +    viewport.setAbovePIDThreshold(false);
 +    abovePIDThreshold.setState(false);
 +
 +    changeColour(viewport.getGlobalColourScheme());
 +
 +    modifyConservation_actionPerformed();
 +  }
 +
 +  public void abovePIDThreshold_actionPerformed()
 +  {
 +    viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
 +
 +    conservationMenuItem.setState(false);
 +    viewport.setConservationSelected(false);
 +
 +    changeColour(viewport.getGlobalColourScheme());
 +
 +    modifyPID_actionPerformed();
 +  }
 +
 +  public void sortPairwiseMenuItem_actionPerformed()
 +  {
 +    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 +    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
 +            .getAlignment().getSequenceAt(0), null);
 +
 +    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
 +            viewport.getAlignment()));
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  public void sortIDMenuItem_actionPerformed()
 +  {
 +    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 +    AlignmentSorter.sortByID(viewport.getAlignment());
-     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
++    addHistoryItem(new OrderCommand("ID Sort", oldOrder,
++            viewport.getAlignment()));
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  public void sortLengthMenuItem_actionPerformed()
 +  {
 +    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 +    AlignmentSorter.sortByLength(viewport.getAlignment());
 +    addHistoryItem(new OrderCommand("Length Sort", oldOrder,
 +            viewport.getAlignment()));
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  public void sortGroupMenuItem_actionPerformed()
 +  {
 +    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 +    AlignmentSorter.sortByGroup(viewport.getAlignment());
 +    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
 +            viewport.getAlignment()));
 +    alignPanel.paintAlignment(true);
 +
 +  }
 +
 +  public void removeRedundancyMenuItem_actionPerformed()
 +  {
 +    new RedundancyPanel(alignPanel);
 +  }
 +
 +  public void pairwiseAlignmentMenuItem_actionPerformed()
 +  {
 +    if (viewport.getSelectionGroup() != null
 +            && viewport.getSelectionGroup().getSize() > 1)
 +    {
 +      Frame frame = new Frame();
 +      frame.add(new PairwiseAlignPanel(alignPanel));
 +      jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
 +              500);
 +    }
 +  }
 +
 +  public void PCAMenuItem_actionPerformed()
 +  {
 +    // are the sequences aligned?
 +    if (!viewport.getAlignment().isAligned(false))
 +    {
 +      SequenceI current;
 +      int Width = viewport.getAlignment().getWidth();
 +
 +      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 +      {
 +        current = viewport.getAlignment().getSequenceAt(i);
 +
 +        if (current.getLength() < Width)
 +        {
 +          current.insertCharAt(Width - 1, viewport.getGapCharacter());
 +        }
 +      }
 +      alignPanel.paintAlignment(true);
 +    }
 +
 +    if ((viewport.getSelectionGroup() != null
 +            && viewport.getSelectionGroup().getSize() < 4 && viewport
 +            .getSelectionGroup().getSize() > 0)
 +            || viewport.getAlignment().getHeight() < 4)
 +    {
 +      return;
 +    }
 +
 +    try
 +    {
 +      new PCAPanel(viewport);
 +    } catch (java.lang.OutOfMemoryError ex)
 +    {
 +    }
 +
 +  }
 +
 +  public void averageDistanceTreeMenuItem_actionPerformed()
 +  {
 +    NewTreePanel("AV", "PID", "Average distance tree using PID");
 +  }
 +
 +  public void neighbourTreeMenuItem_actionPerformed()
 +  {
 +    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
 +  }
 +
 +  protected void njTreeBlosumMenuItem_actionPerformed()
 +  {
 +    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
 +  }
 +
 +  protected void avTreeBlosumMenuItem_actionPerformed()
 +  {
 +    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
 +  }
 +
 +  void NewTreePanel(String type, String pwType, String title)
 +  {
 +    // are the sequences aligned?
 +    if (!viewport.getAlignment().isAligned(false))
 +    {
 +      SequenceI current;
 +      int Width = viewport.getAlignment().getWidth();
 +
 +      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 +      {
 +        current = viewport.getAlignment().getSequenceAt(i);
 +
 +        if (current.getLength() < Width)
 +        {
 +          current.insertCharAt(Width - 1, viewport.getGapCharacter());
 +        }
 +      }
 +      alignPanel.paintAlignment(true);
 +
 +    }
 +
 +    if ((viewport.getSelectionGroup() != null && viewport
 +            .getSelectionGroup().getSize() > 1)
-             || (viewport.getSelectionGroup() == null && viewport.getAlignment()
-                     .getHeight() > 1))
++            || (viewport.getAlignment().getHeight() > 1))
 +    {
 +      final TreePanel tp = new TreePanel(alignPanel, type, pwType);
 +
 +      addTreeMenuItem(tp, title);
 +
 +      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
 +    }
 +  }
 +
 +  void loadTree_actionPerformed()
 +  {
 +    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
 +    cap.setText("Paste your Newick tree file here.");
 +    cap.setTreeImport();
 +    Frame frame = new Frame();
 +    frame.add(cap);
 +    jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
 +  }
 +
 +  public void loadTree(jalview.io.NewickFile tree, String treeFile)
 +  {
 +    TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
 +    jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
 +    addTreeMenuItem(tp, treeFile);
 +  }
 +
 +  /**
 +   * sort the alignment using the given treePanel
-    *
++   * 
 +   * @param treePanel
 +   *          tree used to sort view
 +   * @param title
 +   *          string used for undo event name
 +   */
 +  public void sortByTree(TreePanel treePanel, String title)
 +  {
 +    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 +    AlignmentSorter
 +            .sortByTree(viewport.getAlignment(), treePanel.getTree());
 +    // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
 +    // HistoryItem.SORT));
 +    addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
 +            viewport.getAlignment()));
 +    alignPanel.paintAlignment(true);
 +  }
 +
 +  /**
 +   * Do any automatic reordering of the alignment and add the necessary bits to
 +   * the menu structure for the new tree
-    *
++   * 
 +   * @param treePanel
 +   * @param title
 +   */
 +  protected void addTreeMenuItem(final TreePanel treePanel,
 +          final String title)
 +  {
 +    final MenuItem item = new MenuItem(title);
 +    sortByTreeMenu.add(item);
 +    item.addActionListener(new java.awt.event.ActionListener()
 +    {
 +      @Override
 +      public void actionPerformed(ActionEvent evt)
 +      {
 +        sortByTree(treePanel, title); // treePanel.getTitle());
 +      }
 +    });
 +
 +    treePanel.addWindowListener(new WindowAdapter()
 +    {
 +      @Override
 +      public void windowOpened(WindowEvent e)
 +      {
 +        if (viewport.sortByTree)
 +        {
 +          sortByTree(treePanel, title);
 +        }
 +        super.windowOpened(e);
 +      }
 +
 +      @Override
 +      public void windowClosing(WindowEvent e)
 +      {
 +        sortByTreeMenu.remove(item);
 +      };
 +    });
 +  }
++
 +  public boolean sortBy(AlignmentOrder alorder, String undoname)
 +  {
-     SequenceI[] oldOrder = viewport.getAlignment()
-     .getSequencesArray();
++    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 +    if (viewport.applet.debug)
 +    {
-       System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
++      System.err.println("Sorting " + alorder.getOrder().size()
++              + " in alignment '" + getTitle() + "'");
 +    }
 +    AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
-     if (undoname!=null)
++    if (undoname != null)
 +    {
-       addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
++      addHistoryItem(new OrderCommand(undoname, oldOrder,
++              viewport.getAlignment()));
 +    }
 +    alignPanel.paintAlignment(true);
 +    return true;
 +  }
 +
 +  protected void documentation_actionPerformed()
 +  {
 +    alignPanel.av.applet.openJalviewHelpUrl();
 +  }
 +
 +  protected void about_actionPerformed()
 +  {
 +
 +    class AboutPanel extends Canvas
 +    {
 +      String version;
 +
 +      String builddate;
 +
 +      public AboutPanel(String version, String builddate)
 +      {
 +        this.version = version;
 +        this.builddate = builddate;
 +      }
 +
 +      @Override
 +      public void paint(Graphics g)
 +      {
 +        g.setColor(Color.white);
 +        g.fillRect(0, 0, getSize().width, getSize().height);
 +        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
 +        FontMetrics fm = g.getFontMetrics();
 +        int fh = fm.getHeight();
 +        int y = 5, x = 7;
 +        g.setColor(Color.black);
 +        // TODO: update this text for each release or centrally store it for
 +        // lite and application
 +        g.setFont(new Font("Helvetica", Font.BOLD, 14));
 +        g.drawString("JalviewLite - Release " + version, x, y += fh);
 +        g.setFont(new Font("Helvetica", Font.BOLD, 12));
 +        g.drawString("Build date: " + builddate, x, y += fh);
 +        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
 +        g.drawString(
-                 "Authors:  Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
++                "Authors:  Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
 +                x, y += fh * 1.5);
-         g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
++        g.drawString(
++                "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",
++                x + 50, y += fh + 8);
 +        g.drawString(
 +                "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
 +                x, y += fh);
 +        g.drawString(
 +                "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
 +                x, y += fh);
 +        g.drawString("If  you use Jalview, please cite:", x, y += fh + 8);
 +        g.drawString(
 +                "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
 +                x, y += fh);
 +        g.drawString(
 +                "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
 +                x, y += fh);
 +        g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
 +                x, y += fh);
 +      }
 +    }
 +
 +    Frame frame = new Frame();
 +    frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
 +            .getBuildDate()));
 +    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
 +
 +  }
 +
 +  public void showURL(String url, String target)
 +  {
 +    if (viewport.applet == null)
 +    {
 +      System.out.println("Not running as applet - no browser available.");
 +    }
 +    else
 +    {
 +      viewport.applet.showURL(url, target);
 +    }
 +  }
 +
 +  // ////////////////////////////////////////////////////////////////////////////////
 +  // JBuilder Graphics here
 +
 +  MenuBar alignFrameMenuBar = new MenuBar();
 +
 +  Menu fileMenu = new Menu("File");
 +
 +  MenuItem loadApplication = new MenuItem("View in Full Application");
 +
 +  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 ...");
 +
 +  MenuItem closeMenuItem = new MenuItem("Close");
 +
 +  Menu editMenu = new Menu("Edit");
 +
 +  Menu viewMenu = new Menu("View");
 +
 +  Menu colourMenu = new Menu("Colour");
 +
 +  Menu calculateMenu = new Menu("Calculate");
 +
 +  MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
 +
 +  MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
 +
 +  MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
 +
 +  MenuItem remove2LeftMenuItem = new MenuItem();
 +
 +  MenuItem remove2RightMenuItem = new MenuItem();
 +
 +  MenuItem removeGappedColumnMenuItem = new MenuItem();
 +
 +  MenuItem removeAllGapsMenuItem = new MenuItem();
 +
 +  CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
 +
 +  CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
 +
 +  MenuItem sortPairwiseMenuItem = new MenuItem();
 +
 +  MenuItem sortIDMenuItem = new MenuItem();
 +
 +  MenuItem sortLengthMenuItem = new MenuItem();
 +
 +  MenuItem sortGroupMenuItem = new MenuItem();
 +
 +  MenuItem removeRedundancyMenuItem = new MenuItem();
 +
 +  MenuItem pairwiseAlignmentMenuItem = new MenuItem();
 +
 +  MenuItem PCAMenuItem = new MenuItem();
 +
 +  MenuItem averageDistanceTreeMenuItem = new MenuItem();
 +
 +  MenuItem neighbourTreeMenuItem = new MenuItem();
 +
 +  BorderLayout borderLayout1 = new BorderLayout();
 +
 +  public Label statusBar = new Label();
 +
 +  Menu outputTextboxMenu = new Menu();
 +
 +  MenuItem clustalColour = new MenuItem();
 +
 +  MenuItem zappoColour = new MenuItem();
 +
 +  MenuItem taylorColour = new MenuItem();
 +
 +  MenuItem hydrophobicityColour = new MenuItem();
 +
 +  MenuItem helixColour = new MenuItem();
 +
 +  MenuItem strandColour = new MenuItem();
 +
 +  MenuItem turnColour = new MenuItem();
 +
 +  MenuItem buriedColour = new MenuItem();
 +
 +  MenuItem purinePyrimidineColour = new MenuItem();
++
 +  MenuItem RNAInteractionColour = 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();
 +
 +  MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
 +
 +  CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
 +
 +  CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
 +
 +  CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
 +
 +  MenuItem alProperties = new MenuItem("Alignment Properties...");
 +
 +  MenuItem overviewMenuItem = new MenuItem();
 +
 +  MenuItem undoMenuItem = new MenuItem();
 +
 +  MenuItem redoMenuItem = new MenuItem();
 +
 +  CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 +
 +  MenuItem noColourmenuItem = new MenuItem();
 +
 +  CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
 +
 +  CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
 +
 +  MenuItem findMenuItem = new MenuItem();
 +
 +  CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
 +
 +  MenuItem nucleotideColour = new MenuItem();
 +
 +  MenuItem deleteGroups = new MenuItem();
 +
 +  MenuItem grpsFromSelection = new MenuItem();
 +
 +  MenuItem delete = new MenuItem();
 +
 +  MenuItem copy = new MenuItem();
 +
 +  MenuItem cut = new MenuItem();
 +
 +  Menu pasteMenu = new Menu();
 +
 +  MenuItem pasteNew = new MenuItem();
 +
 +  MenuItem pasteThis = new MenuItem();
 +
 +  CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
 +
 +  MenuItem font = new MenuItem();
 +
 +  CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
 +
 +  CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
 +
 +  CheckboxMenuItem scaleRight = new CheckboxMenuItem();
 +
 +  MenuItem modifyPID = new MenuItem();
 +
 +  MenuItem modifyConservation = new MenuItem();
 +
 +  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();
 +
 +  Menu calculate = new Menu();
 +
 +  MenuItem inputText = new MenuItem();
 +
 +  Menu helpMenu = new Menu();
 +
 +  MenuItem documentation = new MenuItem();
 +
 +  MenuItem about = new MenuItem();
 +
 +  CheckboxMenuItem seqLimits = new CheckboxMenuItem();
 +
 +  CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
 +
 +  CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
-   Menu autoAnnMenu=new Menu();
-   CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
++
++  Menu autoAnnMenu = new Menu();
++
++  CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
++
 +  CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
++
 +  CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
++
 +  CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
++
 +  CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
 +
++  CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
++
 +  private void jbInit() throws Exception
 +  {
 +
 +    setMenuBar(alignFrameMenuBar);
 +
 +    MenuItem item;
 +
 +    // dynamically fill save as menu with available formats
 +    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
 +    {
 +
 +      item = new MenuItem(
 +              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 +
 +      item.addActionListener(new java.awt.event.ActionListener()
 +      {
 +        @Override
 +        public void actionPerformed(ActionEvent e)
 +        {
 +          outputText_actionPerformed(e);
 +        }
 +      });
 +
 +      outputTextboxMenu.add(item);
 +    }
 +    closeMenuItem.addActionListener(this);
 +    loadApplication.addActionListener(this);
 +
 +    loadTree.addActionListener(this);
 +    loadAnnotations.addActionListener(this);
 +    outputFeatures.addActionListener(this);
 +    outputAnnotations.addActionListener(this);
 +    selectAllSequenceMenuItem.addActionListener(this);
 +    deselectAllSequenceMenuItem.addActionListener(this);
 +    invertSequenceMenuItem.addActionListener(this);
 +    remove2LeftMenuItem.setLabel("Remove Left");
 +    remove2LeftMenuItem.addActionListener(this);
 +    remove2RightMenuItem.setLabel("Remove Right");
 +    remove2RightMenuItem.addActionListener(this);
 +    removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
 +    removeGappedColumnMenuItem.addActionListener(this);
 +    removeAllGapsMenuItem.setLabel("Remove All Gaps");
 +    removeAllGapsMenuItem.addActionListener(this);
 +    viewBoxesMenuItem.setLabel("Boxes");
 +    viewBoxesMenuItem.setState(true);
 +    viewBoxesMenuItem.addItemListener(this);
 +    viewTextMenuItem.setLabel("Text");
 +    viewTextMenuItem.setState(true);
 +    viewTextMenuItem.addItemListener(this);
 +    sortPairwiseMenuItem.setLabel("by Pairwise Identity");
 +    sortPairwiseMenuItem.addActionListener(this);
 +    sortIDMenuItem.setLabel("by ID");
 +    sortIDMenuItem.addActionListener(this);
 +    sortLengthMenuItem.setLabel("by Length");
 +    sortLengthMenuItem.addActionListener(this);
 +    sortGroupMenuItem.setLabel("by Group");
 +    sortGroupMenuItem.addActionListener(this);
 +    removeRedundancyMenuItem.setLabel("Remove Redundancy...");
 +    removeRedundancyMenuItem.addActionListener(this);
 +    pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
 +    pairwiseAlignmentMenuItem.addActionListener(this);
 +    PCAMenuItem.setLabel("Principal Component Analysis");
 +    PCAMenuItem.addActionListener(this);
 +    averageDistanceTreeMenuItem
 +            .setLabel("Average Distance Using % Identity");
 +    averageDistanceTreeMenuItem.addActionListener(this);
 +    neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
 +    neighbourTreeMenuItem.addActionListener(this);
 +    statusBar.setBackground(Color.white);
 +    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 +    statusBar.setText("Status bar");
 +    outputTextboxMenu.setLabel("Output to Textbox");
 +    clustalColour.setLabel("Clustalx");
 +
 +    clustalColour.addActionListener(this);
 +    zappoColour.setLabel("Zappo");
 +    zappoColour.addActionListener(this);
 +    taylorColour.setLabel("Taylor");
 +    taylorColour.addActionListener(this);
 +    hydrophobicityColour.setLabel("Hydrophobicity");
 +    hydrophobicityColour.addActionListener(this);
 +    helixColour.setLabel("Helix Propensity");
 +    helixColour.addActionListener(this);
 +    strandColour.setLabel("Strand Propensity");
 +    strandColour.addActionListener(this);
 +    turnColour.setLabel("Turn Propensity");
 +    turnColour.addActionListener(this);
 +    buriedColour.setLabel("Buried Index");
 +    buriedColour.addActionListener(this);
 +    purinePyrimidineColour.setLabel("Purine/Pyrimidine");
 +    purinePyrimidineColour.addActionListener(this);
 +    RNAInteractionColour.setLabel("Purine/Pyrimidine");
 +    RNAInteractionColour.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);
 +    tcoffeeColour.setLabel("T-Coffee Scores");
-     tcoffeeColour.setEnabled(false);	// it will enabled only if a score file is provided
++    tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
++                                     // provided
 +    tcoffeeColour.addActionListener(this);
-     avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
++    avDistanceTreeBlosumMenuItem
++            .setLabel("Average Distance Using BLOSUM62");
 +    avDistanceTreeBlosumMenuItem.addActionListener(this);
 +    njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
 +    njTreeBlosumMenuItem.addActionListener(this);
 +    annotationPanelMenuItem.setLabel("Show Annotations");
 +    annotationPanelMenuItem.addItemListener(this);
 +    colourTextMenuItem.setLabel("Colour Text");
 +    colourTextMenuItem.addItemListener(this);
 +    displayNonconservedMenuItem.setLabel("Show nonconserved");
 +    displayNonconservedMenuItem.addItemListener(this);
 +    alProperties.addActionListener(this);
 +    overviewMenuItem.setLabel("Overview Window");
 +    overviewMenuItem.addActionListener(this);
 +    undoMenuItem.setEnabled(false);
 +    undoMenuItem.setLabel("Undo");
 +    undoMenuItem.addActionListener(this);
 +    redoMenuItem.setEnabled(false);
 +    redoMenuItem.setLabel("Redo");
 +    redoMenuItem.addActionListener(this);
 +    conservationMenuItem.setLabel("by Conservation");
 +    conservationMenuItem.addItemListener(this);
 +    noColourmenuItem.setLabel("None");
 +    noColourmenuItem.addActionListener(this);
 +    wrapMenuItem.setLabel("Wrap");
 +    wrapMenuItem.addItemListener(this);
 +    renderGapsMenuItem.setLabel("Show Gaps");
 +    renderGapsMenuItem.setState(true);
 +    renderGapsMenuItem.addItemListener(this);
 +    findMenuItem.setLabel("Find...");
 +    findMenuItem.addActionListener(this);
 +    abovePIDThreshold.setLabel("Above Identity Threshold");
 +    abovePIDThreshold.addItemListener(this);
 +    nucleotideColour.setLabel("Nucleotide");
 +    nucleotideColour.addActionListener(this);
 +    deleteGroups.setLabel("Undefine Groups");
 +    deleteGroups.addActionListener(this);
 +    grpsFromSelection.setLabel("Make Groups for selection");
 +    grpsFromSelection.addActionListener(this);
 +    copy.setLabel("Copy");
 +    copy.addActionListener(this);
 +    cut.setLabel("Cut");
 +    cut.addActionListener(this);
 +    delete.setLabel("Delete");
 +    delete.addActionListener(this);
 +    pasteMenu.setLabel("Paste");
 +    pasteNew.setLabel("To New Alignment");
 +    pasteNew.addActionListener(this);
 +    pasteThis.setLabel("Add To This Alignment");
 +    pasteThis.addActionListener(this);
 +    applyToAllGroups.setLabel("Apply Colour To All Groups");
 +    applyToAllGroups.setState(true);
 +    applyToAllGroups.addItemListener(this);
 +    font.setLabel("Font...");
 +    font.addActionListener(this);
 +    scaleAbove.setLabel("Scale Above");
 +    scaleAbove.setState(true);
 +    scaleAbove.setEnabled(false);
 +    scaleAbove.addItemListener(this);
 +    scaleLeft.setEnabled(false);
 +    scaleLeft.setState(true);
 +    scaleLeft.setLabel("Scale Left");
 +    scaleLeft.addItemListener(this);
 +    scaleRight.setEnabled(false);
 +    scaleRight.setState(true);
 +    scaleRight.setLabel("Scale Right");
 +    scaleRight.addItemListener(this);
 +    modifyPID.setLabel("Modify Identity Threshold...");
 +    modifyPID.addActionListener(this);
 +    modifyConservation.setLabel("Modify Conservation Threshold...");
 +    modifyConservation.addActionListener(this);
 +    sortByTreeMenu.setLabel("By Tree Order");
 +    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");
 +    centreColumnLabelFlag.addItemListener(this);
 +    followMouseOverFlag.setLabel("Automatic Scrolling");
 +    followMouseOverFlag.addItemListener(this);
 +    helpMenu.setLabel("Help");
 +    documentation.setLabel("Documentation");
 +    documentation.addActionListener(this);
 +
 +    about.setLabel("About...");
 +    about.addActionListener(this);
 +    seqLimits.setState(true);
 +    seqLimits.setLabel("Show Sequence Limits");
 +    seqLimits.addItemListener(this);
 +    featureSettings.setLabel("Feature Settings...");
 +    featureSettings.addActionListener(this);
 +    sequenceFeatures.setLabel("Sequence Features");
 +    sequenceFeatures.addItemListener(this);
 +    sequenceFeatures.setState(false);
 +    annotationColour.setLabel("by Annotation...");
 +    annotationColour.addActionListener(this);
 +    invertSequenceMenuItem.setLabel("Invert Sequence Selection");
 +    invertColSel.setLabel("Invert Column Selection");
 +    menu1.setLabel("Show");
 +    showColumns.setLabel("All Columns ");
 +    showSeqs.setLabel("All Sequences");
 +    menu2.setLabel("Hide");
 +    hideColumns.setLabel("Selected Columns");
 +    hideSequences.setLabel("Selected Sequences");
 +    hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
 +    hideAllSelection.setLabel("Selected Region");
 +    showAllHidden.setLabel("All Sequences and Columns");
 +    showGroupConsensus.setLabel("Group Consensus");
 +    showGroupConservation.setLabel("Group Conservation");
 +    showConsensusHistogram.setLabel("Show Consensus Histogram");
 +    showSequenceLogo.setLabel("Show Consensus Logo");
++    normSequenceLogo.setLabel("Normalise Consensus Logo");
 +    applyAutoAnnotationSettings.setLabel("Apply to all groups");
 +    applyAutoAnnotationSettings.setState(true);
 +    autoAnnMenu.setLabel("Autocalculated Annotation");
 +
 +    invertColSel.addActionListener(this);
 +    showColumns.addActionListener(this);
 +    showSeqs.addActionListener(this);
 +    hideColumns.addActionListener(this);
 +    hideSequences.addActionListener(this);
 +    hideAllButSelection.addActionListener(this);
 +    hideAllSelection.addActionListener(this);
 +    showAllHidden.addActionListener(this);
 +    showGroupConsensus.addItemListener(this);
 +    showGroupConservation.addItemListener(this);
 +    showConsensusHistogram.addItemListener(this);
 +    showSequenceLogo.addItemListener(this);
 +    applyAutoAnnotationSettings.addItemListener(this);
 +    formatMenu.setLabel("Format");
 +    selectMenu.setLabel("Select");
 +    newView.setLabel("New View");
 +    newView.addActionListener(this);
 +    alignFrameMenuBar.add(fileMenu);
 +    alignFrameMenuBar.add(editMenu);
 +    alignFrameMenuBar.add(selectMenu);
 +    alignFrameMenuBar.add(viewMenu);
 +    alignFrameMenuBar.add(formatMenu);
 +    alignFrameMenuBar.add(colourMenu);
 +    alignFrameMenuBar.add(calculateMenu);
 +    alignFrameMenuBar.add(helpMenu);
 +
 +    fileMenu.add(inputText);
 +    fileMenu.add(loadTree);
 +    fileMenu.add(loadAnnotations);
 +
 +    fileMenu.addSeparator();
 +    fileMenu.add(outputTextboxMenu);
 +    fileMenu.add(outputFeatures);
 +    fileMenu.add(outputAnnotations);
 +
 +    if (jalviewServletURL != null)
 +    {
 +      fileMenu.add(loadApplication);
 +    }
 +
 +    fileMenu.addSeparator();
 +    fileMenu.add(closeMenuItem);
 +
 +    editMenu.add(undoMenuItem);
 +    editMenu.add(redoMenuItem);
 +    editMenu.add(cut);
 +    editMenu.add(copy);
 +    editMenu.add(pasteMenu);
 +    editMenu.add(delete);
 +    editMenu.addSeparator();
 +    editMenu.add(remove2LeftMenuItem);
 +    editMenu.add(remove2RightMenuItem);
 +    editMenu.add(removeGappedColumnMenuItem);
 +    editMenu.add(removeAllGapsMenuItem);
 +    editMenu.add(removeRedundancyMenuItem);
 +    viewMenu.add(newView);
 +    viewMenu.addSeparator();
 +    viewMenu.add(menu1);
 +    viewMenu.add(menu2);
 +    viewMenu.addSeparator();
 +    viewMenu.add(followMouseOverFlag);
 +    viewMenu.add(annotationPanelMenuItem);
 +    autoAnnMenu.add(applyAutoAnnotationSettings);
 +    autoAnnMenu.add(showConsensusHistogram);
 +    autoAnnMenu.add(showSequenceLogo);
++    autoAnnMenu.add(normSequenceLogo);
 +    autoAnnMenu.addSeparator();
 +    autoAnnMenu.add(showGroupConservation);
 +    autoAnnMenu.add(showGroupConsensus);
 +    viewMenu.add(autoAnnMenu);
 +    viewMenu.addSeparator();
 +    viewMenu.add(sequenceFeatures);
 +    viewMenu.add(featureSettings);
 +    viewMenu.addSeparator();
 +    viewMenu.add(alProperties);
 +    viewMenu.addSeparator();
 +    viewMenu.add(overviewMenuItem);
 +    colourMenu.add(applyToAllGroups);
 +    colourMenu.addSeparator();
 +    colourMenu.add(noColourmenuItem);
 +    colourMenu.add(clustalColour);
 +    colourMenu.add(BLOSUM62Colour);
 +    colourMenu.add(PIDColour);
 +    colourMenu.add(zappoColour);
 +    colourMenu.add(taylorColour);
 +    colourMenu.add(hydrophobicityColour);
 +    colourMenu.add(helixColour);
 +    colourMenu.add(strandColour);
 +    colourMenu.add(turnColour);
 +    colourMenu.add(buriedColour);
 +    colourMenu.add(nucleotideColour);
 +    colourMenu.add(purinePyrimidineColour);
 +    colourMenu.add(RNAInteractionColour);
 +    colourMenu.add(tcoffeeColour);
 +    colourMenu.add(userDefinedColour);
 +    colourMenu.addSeparator();
 +    colourMenu.add(conservationMenuItem);
 +    colourMenu.add(modifyConservation);
 +    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);
 +    sort.add(sortIDMenuItem);
 +    sort.add(sortLengthMenuItem);
 +    sort.add(sortByTreeMenu);
 +    sort.add(sortGroupMenuItem);
 +    sort.add(sortPairwiseMenuItem);
 +    calculate.add(averageDistanceTreeMenuItem);
 +    calculate.add(neighbourTreeMenuItem);
 +    calculate.add(avDistanceTreeBlosumMenuItem);
 +    calculate.add(njTreeBlosumMenuItem);
 +    helpMenu.add(documentation);
 +    helpMenu.add(about);
 +    menu1.add(showColumns);
 +    menu1.add(showSeqs);
 +    menu1.add(showAllHidden);
 +    menu2.add(hideColumns);
 +    menu2.add(hideSequences);
 +    menu2.add(hideAllSelection);
 +    menu2.add(hideAllButSelection);
 +    formatMenu.add(font);
 +    formatMenu.add(seqLimits);
 +    formatMenu.add(wrapMenuItem);
 +    formatMenu.add(scaleAbove);
 +    formatMenu.add(scaleLeft);
 +    formatMenu.add(scaleRight);
 +    formatMenu.add(viewBoxesMenuItem);
 +    formatMenu.add(viewTextMenuItem);
 +    formatMenu.add(colourTextMenuItem);
 +    formatMenu.add(displayNonconservedMenuItem);
 +    formatMenu.add(renderGapsMenuItem);
 +    formatMenu.add(centreColumnLabelFlag);
 +    selectMenu.add(findMenuItem);
 +    selectMenu.addSeparator();
 +    selectMenu.add(selectAllSequenceMenuItem);
 +    selectMenu.add(deselectAllSequenceMenuItem);
 +    selectMenu.add(invertSequenceMenuItem);
 +    selectMenu.add(invertColSel);
 +    selectMenu.add(grpsFromSelection);
 +    selectMenu.add(deleteGroups);
 +
 +  }
 +
 +  MenuItem featureSettings = new MenuItem();
 +
 +  CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
 +
 +  MenuItem annotationColour = new MenuItem();
 +
 +  MenuItem invertColSel = new MenuItem();
 +
 +  Menu menu1 = new Menu();
 +
 +  MenuItem showColumns = new MenuItem();
 +
 +  MenuItem showSeqs = new MenuItem();
 +
 +  Menu menu2 = new Menu();
 +
 +  MenuItem hideColumns = new MenuItem();
 +
 +  MenuItem hideSequences = new MenuItem();
 +
 +  MenuItem hideAllButSelection = new MenuItem();
 +
 +  MenuItem hideAllSelection = new MenuItem();
 +
 +  MenuItem showAllHidden = new MenuItem();
 +
 +  Menu formatMenu = new Menu();
 +
 +  Menu selectMenu = new Menu();
 +
 +  MenuItem newView = new MenuItem();
 +
 +  /**
 +   * Attach the alignFrame panels after embedding menus, if necessary. This used
 +   * to be called setEmbedded, but is now creates the dropdown menus in a
 +   * platform independent manner to avoid OSX/Mac menu appendage daftness.
-    *
++   * 
 +   * @param reallyEmbedded
 +   *          true to attach the view to the applet area on the page rather than
 +   *          in a new window
 +   */
 +  public void createAlignFrameWindow(boolean reallyEmbedded, String title)
 +  {
 +    if (reallyEmbedded)
 +    {
 +      // ////
 +      // Explicly build the embedded menu panel for the on-page applet
 +      //
 +      // view cannot be closed if its actually on the page
 +      fileMenu.remove(closeMenuItem);
 +      fileMenu.remove(3); // Remove Seperator
 +      embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
 +              Font.PLAIN, 10, false); // use our own fonts.
 +      // and actually add the components to the applet area
 +      viewport.applet.setLayout(new BorderLayout());
 +      viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
 +      viewport.applet.add(statusBar, BorderLayout.SOUTH);
 +      alignPanel.setSize(viewport.applet.getSize().width,
 +              viewport.applet.getSize().height - embeddedMenu.HEIGHT
 +                      - statusBar.HEIGHT);
 +      viewport.applet.add(alignPanel, BorderLayout.CENTER);
 +      final AlignFrame me = this;
 +      viewport.applet.addFocusListener(new FocusListener()
 +      {
 +
 +        @Override
 +        public void focusLost(FocusEvent e)
 +        {
-           if (me.viewport.applet.currentAlignFrame==me) {
-                   me.viewport.applet.currentAlignFrame = null;
-         }}
++          if (me.viewport.applet.currentAlignFrame == me)
++          {
++            me.viewport.applet.currentAlignFrame = null;
++          }
++        }
 +
 +        @Override
 +        public void focusGained(FocusEvent e)
 +        {
 +          me.viewport.applet.currentAlignFrame = me;
 +        }
 +      });
 +      viewport.applet.validate();
 +    }
 +    else
 +    {
 +      // //////
 +      // test and embed menu bar if necessary.
 +      //
 +      if (embedMenuIfNeeded(alignPanel))
 +      {
 +        // adjust for status bar height too
 +        alignPanel.setSize(getSize().width, getSize().height
 +                - statusBar.HEIGHT);
 +      }
 +      add(statusBar, BorderLayout.SOUTH);
 +      add(alignPanel, BorderLayout.CENTER);
 +      // and register with the applet so it can pass external API calls to us
 +      jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
 +              DEFAULT_HEIGHT);
 +    }
 +  }
 +
 +  /**
 +   * create a new binding between structures in an existing jmol viewer instance
 +   * and an alignpanel with sequences that have existing PDBFile entries. Note,
 +   * this does not open a new Jmol window, or modify the display of the
 +   * structures in the original jmol window. Note This method doesn't work
 +   * without an additional javascript library to exchange messages between the
 +   * distinct applets. See http://issues.jalview.org/browse/JAL-621
-    *
++   * 
 +   * @param viewer
 +   *          JmolViewer instance
 +   * @param sequenceIds
 +   *          - sequence Ids to search for associations
 +   */
 +  public SequenceStructureBinding addStructureViewInstance(
 +          Object jmolviewer, String[] sequenceIds)
 +  {
 +    org.jmol.api.JmolViewer viewer = null;
 +    try
 +    {
 +      viewer = (org.jmol.api.JmolViewer) jmolviewer;
 +    } catch (ClassCastException ex)
 +    {
 +      System.err.println("Unsupported viewer object :"
 +              + jmolviewer.getClass());
 +    }
 +    if (viewer == null)
 +    {
 +      System.err.println("Can't use this object as a structure viewer:"
 +              + jmolviewer.getClass());
 +      return null;
 +    }
 +    SequenceI[] seqs = null;
 +    if (sequenceIds == null || sequenceIds.length == 0)
 +    {
 +      seqs = viewport.getAlignment().getSequencesArray();
 +    }
 +    else
 +    {
 +      Vector sqi = new Vector();
 +      AlignmentI al = viewport.getAlignment();
 +      for (int sid = 0; sid < sequenceIds.length; sid++)
 +      {
 +        SequenceI sq = al.findName(sequenceIds[sid]);
 +        if (sq != null)
 +        {
 +          sqi.addElement(sq);
 +        }
 +      }
 +      if (sqi.size() > 0)
 +      {
 +        seqs = new SequenceI[sqi.size()];
 +        for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
 +        {
 +          seqs[sid] = (SequenceI) sqi.elementAt(sid);
 +        }
 +      }
 +      else
 +      {
 +        return null;
 +      }
 +    }
 +    ExtJmol jmv = null;
 +    // TODO: search for a jmv that involves viewer
 +    if (jmv == null)
 +    { // create a new viewer/jalview binding.
-       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
++      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
++      { seqs });
 +    }
 +    return jmv;
 +
 +  }
++
 +  /**
 +   * bind a pdb file to a sequence in the current view
-    *
++   * 
 +   * @param sequenceId
 +   *          - sequenceId within the dataset.
 +   * @param pdbEntryString
 +   *          - the short name for the PDB file
 +   * @param pdbFile
 +   *          - pdb file - either a URL or a valid PDB file.
 +   * @return true if binding was as success TODO: consider making an exception
 +   *         structure for indicating when PDB parsing or sequenceId location
 +   *         fails.
 +   */
 +  public boolean addPdbFile(String sequenceId, String pdbEntryString,
 +          String pdbFile)
 +  {
 +    SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
 +    boolean needtoadd = false;
 +    if (toaddpdb != null)
 +    {
 +      Vector pdbe = toaddpdb.getPDBId();
 +      PDBEntry pdbentry = null;
 +      if (pdbe != null && pdbe.size() > 0)
 +      {
 +        for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
 +        {
 +          pdbentry = (PDBEntry) pdbe.elementAt(pe);
 +          if (!pdbentry.getId().equals(pdbEntryString)
 +                  && !pdbentry.getFile().equals(pdbFile))
 +          {
 +            pdbentry = null;
 +          }
 +          else
 +          {
 +            continue;
 +          }
 +        }
 +      }
 +      if (pdbentry == null)
 +      {
 +        pdbentry = new PDBEntry();
 +        pdbentry.setId(pdbEntryString);
 +        pdbentry.setFile(pdbFile);
 +        needtoadd = true; // add this new entry to sequence.
 +      }
 +      // resolve data source
 +      // TODO: this code should be a refactored to an io package
 +      String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
 +      if (protocol == null)
 +      {
 +        return false;
 +      }
 +      if (needtoadd)
 +      {
 +        // make a note of the access mode and add
 +        if (pdbentry.getProperty() == null)
 +        {
 +          pdbentry.setProperty(new Hashtable());
 +        }
 +        pdbentry.getProperty().put("protocol", protocol);
 +        toaddpdb.addPDBId(pdbentry);
 +      }
 +    }
 +    return true;
 +  }
 +
 +  private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
 +  {
 +    if (seqs != null)
 +    {
 +      Vector sequences = new Vector();
 +      for (int i = 0; i < seqs.length; i++)
 +      {
 +        if (seqs[i] != null)
 +        {
 +          sequences.addElement(new Object[]
 +          { seqs[i], (chains != null) ? chains[i] : null });
 +        }
 +      }
 +      seqs = new SequenceI[sequences.size()];
 +      chains = new String[sequences.size()];
 +      for (int i = 0, isize = sequences.size(); i < isize; i++)
 +      {
 +        Object[] oj = (Object[]) sequences.elementAt(i);
 +
 +        seqs[i] = (SequenceI) oj[0];
 +        chains[i] = (String) oj[1];
 +      }
 +    }
 +    return new Object[]
 +    { seqs, chains };
 +
 +  }
 +
 +  public void newStructureView(JalviewLite applet, PDBEntry pdb,
 +          SequenceI[] seqs, String[] chains, String protocol)
 +  {
 +    // Scrub any null sequences from the array
 +    Object[] sqch = cleanSeqChainArrays(seqs, chains);
 +    seqs = (SequenceI[]) sqch[0];
 +    chains = (String[]) sqch[1];
 +    if (seqs == null || seqs.length == 0)
 +    {
 +      System.err
 +              .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
 +    }
 +    if (protocol == null || protocol.trim().length() == 0
 +            || protocol.equals("null"))
 +    {
 +      protocol = (String) pdb.getProperty().get("protocol");
 +      if (protocol == null)
 +      {
 +        System.err.println("Couldn't work out protocol to open structure: "
 +                + pdb.getId());
 +        return;
 +      }
 +    }
 +    if (applet.useXtrnalSviewer)
 +    {
 +      // register the association(s) and quit, don't create any windows.
-       if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
-         System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
++      if (StructureSelectionManager.getStructureSelectionManager(applet)
++              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
++      {
++        System.err.println("Failed to map " + pdb.getFile() + " ("
++                + protocol + ") to any sequences");
 +      }
 +      return;
 +    }
 +    if (applet.isAlignPdbStructures() && applet.jmolAvailable)
 +    {
 +      // can only do alignments with Jmol
 +      // find the last jmol window assigned to this alignment
 +      jalview.appletgui.AppletJmol ajm = null, tajm;
 +      Vector jmols = applet
 +              .getAppletWindow(jalview.appletgui.AppletJmol.class);
 +      for (int i = 0, iSize = jmols.size(); i < iSize; i++)
 +      {
 +        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
 +        if (tajm.ap.alignFrame == this)
 +        {
 +          ajm = tajm;
 +          break;
 +        }
 +      }
 +      if (ajm != null)
 +      {
 +        System.err
 +                .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
 +        // try and add the pdb structure
 +        // ajm.addS
 +        ajm = null;
 +      }
 +    }
 +    // otherwise, create a new window
 +    if (applet.jmolAvailable)
 +    {
 +      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
 +              protocol);
 +      applet.lastFrameX += 40;
 +      applet.lastFrameY += 40;
 +    }
 +    else
 +    {
 +      new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
 +    }
 +
 +  }
 +
 +  public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
 +          SequenceI[][] seqs, String[][] chains, String[] protocols)
 +  {
 +    // TODO Auto-generated method stub
 +    System.err.println("Aligned Structure View: Not yet implemented.");
 +  }
 +
 +  /**
-    * modify the current selection, providing the user has not made a selection already.
-    * @param sel - sequences from this alignment
-    * @param csel - columns to be selected on the alignment
++   * modify the current selection, providing the user has not made a selection
++   * already.
++   * 
++   * @param sel
++   *          - sequences from this alignment
++   * @param csel
++   *          - columns to be selected on the alignment
 +   */
 +  public void select(SequenceGroup sel, ColumnSelection csel)
 +  {
 +    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() {
++  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
++   * 
++   * @param source
++   *          File/URL/T-COFFEE score file contents
 +   * @throws IOException
 +   * @return true if alignment was annotated with data from source
-  * @throws SAXException 
-  * @throws ParserConfigurationException 
-  * @throws ExceptionFileFormatOrSyntax 
-  * @throws ExceptionLoadingFailed 
-  * @throws ExceptionPermissionDenied 
-  * @throws InterruptedException 
-  * @throws ExceptionUnmatchedClosingParentheses 
++   * @throws SAXException
++   * @throws ParserConfigurationException
++   * @throws ExceptionFileFormatOrSyntax
++   * @throws ExceptionLoadingFailed
++   * @throws ExceptionPermissionDenied
++   * @throws InterruptedException
++   * @throws ExceptionUnmatchedClosingParentheses
 +   */
-   public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
- 
-     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;
-   }
++  public boolean loadScoreFile(String source) throws IOException,
++          ExceptionFileFormatOrSyntax, ParserConfigurationException,
++          SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
++          InterruptedException, ExceptionUnmatchedClosingParentheses
++  {
++
++    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;
++  }
 +
 +}
diff --cc src/jalview/datamodel/Sequence.java
index d82775c,580c850..5315d1a
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@@ -1181,21 -1180,24 +1184,29 @@@ public class Sequence implements Sequen
    }
  
    /**
-    * @return The index (zero-based) on this sequence in the MSA. 
-    * It returns {@code -1} if this information is not available.
+    * @return The index (zero-based) on this sequence in the MSA. It returns
+    *         {@code -1} if this information is not available.
     */
-   public int getIndex() { return index; }
-   
+   public int getIndex()
+   {
+     return index;
+   }
+ 
    /**
-    * Defines the position of this sequence in the MSA. 
-    * Use the value {@code -1} if this information is undefined.
+    * Defines the position of this sequence in the MSA. Use the value {@code -1}
+    * if this information is undefined.
     * 
-    * @param The position for this sequence. This value is zero-based (zero for this first sequence)
+    * @param The
+    *          position for this sequence. This value is zero-based (zero for
+    *          this first sequence)
     */
-   public void setIndex(int value) { index = value; }
+   public void setIndex(int value)
+   {
+     index = value;
+   }
 +  
 +  public void setRNA(RNA r){rna=r;}
 +  
 +  public RNA getRNA() { return rna; }
 +  
  }
diff --cc src/jalview/ext/varna/VarnaCommands.java
index 60c1912,527a847..21f626f
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@@ -1,143 -1,167 +1,157 @@@
- /**
 -/*
 - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
 - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 - * 
 - * This file is part of Jalview.
 - * 
 - * Jalview is free software: you can redistribute it and/or
 - * modify it under the terms of the GNU General Public License 
 - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 - *  
 - * Jalview is distributed in the hope that it will be useful, but 
 - * WITHOUT ANY WARRANTY; without even the implied warranty 
 - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 - * PURPOSE.  See the GNU General Public License for more details.
 - * 
 - * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 - */
 -package jalview.ext.varna;
 -
 -import jalview.api.FeatureRenderer;
 -import jalview.api.SequenceRenderer;
 -import jalview.datamodel.AlignmentI;
 -import jalview.datamodel.SequenceI;
 -import jalview.structure.StructureMapping;
 -import jalview.structure.StructureSelectionManager;
 -
 -import java.awt.Color;
 -import java.util.ArrayList;
 -
 -/**
 - * Routines for generating Jmol commands for Jalview/Jmol binding another
 - * cruisecontrol test.
 - * 
 - * @author JimP
 - * 
 - */
 -public class VarnaCommands
 -{
 -
 -  /**
 -   * Jmol utility which constructs the commands to colour chains by the given
 -   * alignment
 -   * 
 -   */
 -  public static String[] getColourBySequenceCommand(
 -          StructureSelectionManager ssm, String[] files,
 -          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
 -          AlignmentI alignment)
 -  {
 -    ArrayList<String> str = new ArrayList<String>();
 -    StringBuffer command = new StringBuffer();
 -
 -    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
 -    {
 -      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
 -
 -      if (mapping == null || mapping.length < 1)
 -        continue;
 -
 -      int lastPos = -1;
 -      for (int s = 0; s < sequence[pdbfnum].length; s++)
 -      {
 -        for (int sp, m = 0; m < mapping.length; m++)
 -        {
 -          if (mapping[m].getSequence() == sequence[pdbfnum][s]
 -                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
 -          {
 -            SequenceI asp = alignment.getSequenceAt(sp);
 -            for (int r = 0; r < asp.getLength(); r++)
 -            {
 -              // no mapping to gaps in sequence
 -              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
 -              {
 -                continue;
 -              }
 -              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 -
 -              if (pos < 1 || pos == lastPos)
 -                continue;
 -
 -              lastPos = pos;
 -
 -              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 -
 -              if (fr != null)
 -                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
 -              String newSelcom = (mapping[m].getChain() != " " ? ":"
 -                      + mapping[m].getChain() : "")
 -                      + "/"
 -                      + (pdbfnum + 1)
 -                      + ".1"
 -                      + ";color["
 -                      + col.getRed()
 -                      + ","
 -                      + col.getGreen()
 -                      + ","
 -                      + col.getBlue() + "]";
 -              if (command.length() > newSelcom.length()
 -                      && command.substring(
 -                              command.length() - newSelcom.length())
 -                              .equals(newSelcom))
 -              {
 -                command = VarnaCommands.condenseCommand(command, pos);
 -                continue;
 -              }
 -              // TODO: deal with case when buffer is too large for Jmol to parse
 -              // - execute command and flush
 -
 -              command.append(";");
 -              if (command.length() > 51200)
 -              {
 -                // add another chunk
 -                str.add(command.toString());
 -                command.setLength(0);
 -              }
 -              command.append("select " + pos);
 -              command.append(newSelcom);
 -            }
 -            break;
 -          }
 -        }
 -      }
 -    }
 -    {
 -      // add final chunk
 -      str.add(command.toString());
 -      command.setLength(0);
 -    }
 -    return str.toArray(new String[str.size()]);
 -  }
 -
 -  public static StringBuffer condenseCommand(StringBuffer command, int pos)
 -  {
 -
 -    // work back to last 'select'
 -    int p = command.length(), q = p;
 -    do
 -    {
 -      p -= 6;
 -      if (p < 1)
 -      {
 -        p = 0;
 -      }
 -      ;
 -    } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 -
 -    StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 -
 -    command = command.delete(0, q + 7);
 -
 -    String start;
 -
 -    if (command.indexOf("-") > -1)
 -    {
 -      start = command.substring(0, command.indexOf("-"));
 -    }
 -    else
 -    {
 -      start = command.substring(0, command.indexOf(":"));
 -    }
 -
 -    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 -
 -    return sb;
 -  }
 -
 -}
++/*
++ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
++ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 + * 
++ * This file is part of Jalview.
++ * 
++ * Jalview is free software: you can redistribute it and/or
++ * modify it under the terms of the GNU General Public License 
++ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
++ *  
++ * Jalview is distributed in the hope that it will be useful, but 
++ * WITHOUT ANY WARRANTY; without even the implied warranty 
++ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
++ * PURPOSE.  See the GNU General Public License for more details.
++ * 
++ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 + */
 +package jalview.ext.varna;
 +
 +import jalview.api.FeatureRenderer;
 +import jalview.api.SequenceRenderer;
 +import jalview.datamodel.AlignmentI;
 +import jalview.datamodel.SequenceI;
 +import jalview.structure.StructureMapping;
 +import jalview.structure.StructureSelectionManager;
 +import jalview.util.Comparison;
 +
 +import java.awt.Color;
 +import java.util.ArrayList;
 +
 +/**
 + * Routines for generating Jmol commands for Jalview/Jmol binding
 + * another cruisecontrol test.
 + * 
 + * @author JimP
 + *
 + */
 +public class VarnaCommands
 +{
 +
 +  /**
 +   * Jmol utility which constructs the commands to colour chains by the given alignment
 +   * 
 +   */
 +  public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)
 +  {
 +	
 +    ArrayList<String> str = new ArrayList<String>();
 +    StringBuffer command = new StringBuffer();
 +  
 +    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
 +    {
 +      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
 +  
 +      if (mapping == null || mapping.length < 1)
 +        continue;
 +  
 +      int lastPos = -1;
 +      for (int s = 0; s < sequence[pdbfnum].length; s++)
 +      {
 +        for (int sp, m = 0; m < mapping.length; m++)
 +        {
 +          if (mapping[m].getSequence() == sequence[pdbfnum][s]
 +                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
 +          {
 +            SequenceI asp = alignment.getSequenceAt(sp);
 +            for (int r = 0; r < asp.getLength(); r++)
 +            {
 +              // no mapping to gaps in sequence
 +              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
 +              {
 +                continue;
 +              }
 +              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 +  
 +              if (pos < 1 || pos == lastPos)
 +                continue;
 +  
 +              lastPos = pos;
 +  
 +              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 +  
 +              if (fr != null)
 +                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
 +              String newSelcom = (mapping[m].getChain() != " " ? ":"
 +                      + mapping[m].getChain() : "")
 +                      + "/"
 +                      + (pdbfnum + 1)
 +                      + ".1"
 +                      + ";color["
 +                      + col.getRed()
 +                      + ","
 +                      + col.getGreen()
 +                      + ","
 +                      + col.getBlue() + "]";
 +              if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))
 +              {
 +                command = VarnaCommands.condenseCommand(command, pos);
 +                continue;
 +              }
 +              // TODO: deal with case when buffer is too large for Jmol to parse
 +              // - execute command and flush
 +  
 +              command.append(";");
 +              if (command.length()>51200)
 +              {
 +                // add another chunk
 +                str.add(command.toString());
 +                command.setLength(0);
 +              }
 +              command.append("select " + pos);
 +              command.append(newSelcom);
 +            }
 +            break;
 +          }
 +        }
 +      }
 +    }
 +    {
 +      // add final chunk
 +      str.add(command.toString());
 +      command.setLength(0);
 +    }
 +    return str.toArray(new String[str.size()]);
 +  }
 +
 +  public static StringBuffer condenseCommand(StringBuffer command, int pos)
 +  {
 +  
 +    // work back to last 'select'
 +    int p=command.length(),q=p;
 +    do {
 +      p-=6;
 +      if (p<1) { p=0; };
 +    } while ((q=command.indexOf("select",p))==-1 && p>0);
 +    
 +    StringBuffer sb = new StringBuffer(command.substring(0,q+7));
 +  
 +    command =  command.delete(0,q+7);
 +  
 +    String start;
 +  
 +    if (command.indexOf("-") > -1)
 +    {
 +      start = command.substring(0, command.indexOf("-"));
 +    }
 +    else
 +    {
 +      start = command.substring(0, command.indexOf(":"));
 +    }
 +  
 +    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 +  
 +    return sb;
 +  }
 +
 +}
diff --cc src/jalview/gui/AppVarna.java
index 00670aa,1a4c7ac..dd570c0
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@@ -73,16 -61,9 +61,16 @@@ public class AppVarna extends JInternal
  
    AlignmentPanel ap;
  
-   public AppVarna(String sname, SequenceI seq, String strucseq, String struc,
-           String name, AlignmentPanel ap)
+   public AppVarna(String sname, SequenceI seq, String strucseq,
+           String struc, String name, AlignmentPanel ap)
    {
 +	  System.out.println("je suis là (AppVarna!!");
 +	  System.out.println("1:"+sname);
 +	  System.out.println("2:"+seq);
 +	  System.out.println("3:"+strucseq);
 +	  System.out.println("4:"+struc);
 +	  System.out.println("5:"+name);
 +	  System.out.println("6:"+ap);
      this.ap = ap;
      ArrayList<RNA> rnaList = new ArrayList<RNA>();
      RNA rna1 = new RNA(name);
@@@ -100,15 -77,12 +88,13 @@@
      {
        e3.printStackTrace();
      }
-     
-     RNA trim = trimRNA(rna1, "trimmed "+sname);
+     RNA trim = trimRNA(rna1, "trimmed " + sname);
      rnaList.add(trim);
      rnaList.add(rna1);
 +    
      rnas.put(seq, rna1);
      rnas.put(seq, trim);
-    
-     rna1.setName(sname+" (with gaps)");
+     rna1.setName(sname + " (with gaps)");
  
      {
        seqs.put(trim, seq);
@@@ -124,11 -98,9 +110,11 @@@
      vab = new AppVarnaBinding(rnaList);
      // vab = new AppVarnaBinding(seq,struc);
      // System.out.println("Hallo: "+name);
-     this.name = sname+" trimmed to "+name;
+     this.name = sname + " trimmed to " + name;
      initVarna();
 +   
      ssm = ap.getStructureSelectionManager();
 +    System.out.println(ssm.toString());
      ssm.addStructureViewerListener(this);
      ssm.addSelectionListener(this);
    }
diff --cc src/jalview/gui/AssociatePdbFileWithSeq.java
index 3bd21b5,6896863..22c891d
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@@ -18,20 -18,9 +18,17 @@@
  package jalview.gui;
  
  import javax.swing.JOptionPane;
 +import javax.xml.parsers.ParserConfigurationException;
 +
 +import org.xml.sax.SAXException;
 +
 +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  
  import jalview.datamodel.PDBEntry;
- import jalview.datamodel.Sequence;
  import jalview.datamodel.SequenceI;
- import jalview.io.FileParse;
- import jalview.io.IdentifyFile;
  
  /**
   * GUI related routines for associating PDB files with sequences
diff --cc src/jalview/gui/PopupMenu.java
index c354964,1a367c5..3b43e6b
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@@ -23,16 -23,7 +23,15 @@@ import java.awt.*
  import java.awt.event.*;
  
  import javax.swing.*;
 +import javax.xml.parsers.ParserConfigurationException;
 +
 +import org.xml.sax.SAXException;
 +
 +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  
- import MCview.*;
  import jalview.analysis.*;
  import jalview.commands.*;
  import jalview.datamodel.*;
@@@ -283,11 -276,10 +286,11 @@@ public class PopupMenu extends JPopupMe
            if (aa[i].getRNAStruc() != null)
            {
              final String rnastruc = aa[i].getRNAStruc();
-             final String structureLine=aa[i].label;
+             final String structureLine = aa[i].label;
              menuItem = new JMenuItem();
-             menuItem.setText("2D RNA "+structureLine);
+             menuItem.setText("2D RNA " + structureLine);
              menuItem.addActionListener(new java.awt.event.ActionListener()
 +            
              {
                public void actionPerformed(ActionEvent e)
                {
@@@ -329,10 -310,9 +332,10 @@@
                  public void actionPerformed(ActionEvent e)
                  {
                    // TODO: VARNA does'nt print gaps in the sequence
 +                
-                   //new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(), seq.getName(), ap);
-                   new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
-                           .getName(), ap);
+                   new AppVarna(seq.getName() + " structure", seq, seq
+                           .getSequenceAsString(), rnastruc, seq.getName(),
+                           ap);
                  }
                });
                viewStructureMenu.add(menuItem);
@@@ -1151,9 -1113,9 +1164,9 @@@
      colourMenu.add(turnColour);
      colourMenu.add(buriedColour);
      colourMenu.add(nucleotideMenuItem);
-     colourMenu.add(RNAInteractionColour);
 -    if (ap.getAlignment().isNucleotide())
 -    {
 -      colourMenu.add(purinePyrimidineColour);
 +    if (ap.getAlignment().isNucleotide()) {
++      colourMenu.add(RNAInteractionColour);
 +    	colourMenu.add(purinePyrimidineColour);
      }
      // colourMenu.add(covariationColour);
      colourMenu.add(userDefinedColour);
diff --cc src/jalview/io/FeaturesFile.java
index ad2cfd7,ea7ac70..abf89d5
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@@ -1,1018 -1,1026 +1,1018 @@@
- /*
-  * 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.
-  * 
-  * Jalview is free software: you can redistribute it and/or
-  * modify it under the terms of the GNU General Public License 
-  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-  * 
-  * Jalview is distributed in the hope that it will be useful, but 
-  * WITHOUT ANY WARRANTY; without even the implied warranty 
-  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
-  * PURPOSE.  See the GNU General Public License for more details.
-  * 
-  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
-  */
+ /*
+  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+  * 
+  * This file is part of Jalview.
+  * 
+  * Jalview is free software: you can redistribute it and/or
+  * modify it under the terms of the GNU General Public License 
+  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+  *  
+  * Jalview is distributed in the hope that it will be useful, but 
+  * WITHOUT ANY WARRANTY; without even the implied warranty 
+  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+  * PURPOSE.  See the GNU General Public License for more details.
+  * 
+  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+  */
 -package jalview.io;
 -
 -import java.io.*;
 -import java.util.*;
 -
 -import jalview.analysis.SequenceIdMatcher;
 -import jalview.datamodel.*;
 -import jalview.schemes.*;
 -import jalview.util.Format;
 -
 -/**
 - * Parse and create Jalview Features files Detects GFF format features files and
 - * parses. Does not implement standard print() - call specific printFeatures or
 - * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object
 - * for the features annotation - this normally works on an exact match.
 - * 
 - * @author AMW
 - * @version $Revision$
 - */
 -public class FeaturesFile extends AlignFile
 -{
 -  /**
 -   * work around for GFF interpretation bug where source string becomes
 -   * description rather than a group
 -   */
 -  private boolean doGffSource = true;
 -
 -  /**
 -   * Creates a new FeaturesFile object.
 -   */
 -  public FeaturesFile()
 -  {
 -  }
 -
 -  /**
 -   * Creates a new FeaturesFile object.
 -   * 
 -   * @param inFile
 -   *          DOCUMENT ME!
 -   * @param type
 -   *          DOCUMENT ME!
 -   * 
 -   * @throws IOException
 -   *           DOCUMENT ME!
 -   */
 -  public FeaturesFile(String inFile, String type) throws IOException
 -  {
 -    super(inFile, type);
 -  }
 -
 -  public FeaturesFile(FileParse source) throws IOException
 -  {
 -    super(source);
 -  }
 -
 -  /**
 -   * Parse GFF or sequence features file using case-independent matching,
 -   * discarding URLs
 -   * 
 -   * @param align
 -   *          - alignment/dataset containing sequences that are to be annotated
 -   * @param colours
 -   *          - hashtable to store feature colour definitions
 -   * @param removeHTML
 -   *          - process html strings into plain text
 -   * @return true if features were added
 -   */
 -  public boolean parse(AlignmentI align, Hashtable colours,
 -          boolean removeHTML)
 -  {
 -    return parse(align, colours, null, removeHTML, false);
 -  }
 -
 -  /**
 -   * Parse GFF or sequence features file optionally using case-independent
 -   * matching, discarding URLs
 -   * 
 -   * @param align
 -   *          - alignment/dataset containing sequences that are to be annotated
 -   * @param colours
 -   *          - hashtable to store feature colour definitions
 -   * @param removeHTML
 -   *          - process html strings into plain text
 -   * @param relaxedIdmatching
 -   *          - when true, ID matches to compound sequence IDs are allowed
 -   * @return true if features were added
 -   */
 -  public boolean parse(AlignmentI align, Map colours, boolean removeHTML,
 -          boolean relaxedIdMatching)
 -  {
 -    return parse(align, colours, null, removeHTML, relaxedIdMatching);
 -  }
 -
 -  /**
 -   * Parse GFF or sequence features file optionally using case-independent
 -   * matching
 -   * 
 -   * @param align
 -   *          - alignment/dataset containing sequences that are to be annotated
 -   * @param colours
 -   *          - hashtable to store feature colour definitions
 -   * @param featureLink
 -   *          - hashtable to store associated URLs
 -   * @param removeHTML
 -   *          - process html strings into plain text
 -   * @return true if features were added
 -   */
 -  public boolean parse(AlignmentI align, Map colours, Map featureLink,
 -          boolean removeHTML)
 -  {
 -    return parse(align, colours, featureLink, removeHTML, false);
 -  }
 -
 -  /**
 -   * /** Parse GFF or sequence features file
 -   * 
 -   * @param align
 -   *          - alignment/dataset containing sequences that are to be annotated
 -   * @param colours
 -   *          - hashtable to store feature colour definitions
 -   * @param featureLink
 -   *          - hashtable to store associated URLs
 -   * @param removeHTML
 -   *          - process html strings into plain text
 -   * @param relaxedIdmatching
 -   *          - when true, ID matches to compound sequence IDs are allowed
 -   * @return true if features were added
 -   */
 -  public boolean parse(AlignmentI align, Map colours, Map featureLink,
 -          boolean removeHTML, boolean relaxedIdmatching)
 -  {
 -
 -    String line = null;
 -    try
 -    {
 -      SequenceI seq = null;
 -      String type, desc, token = null;
 -
 -      int index, start, end;
 -      float score;
 -      StringTokenizer st;
 -      SequenceFeature sf;
 -      String featureGroup = null, groupLink = null;
 -      Map typeLink = new Hashtable();
 -      /**
 -       * when true, assume GFF style features rather than Jalview style.
 -       */
 -      boolean GFFFile = true;
 -      while ((line = nextLine()) != null)
 -      {
 -        if (line.startsWith("#"))
 -        {
 -          continue;
 -        }
 -
 -        st = new StringTokenizer(line, "\t");
 -        if (st.countTokens() == 1)
 -        {
 -          if (line.trim().equalsIgnoreCase("GFF"))
 -          {
 -            // Start parsing file as if it might be GFF again.
 -            GFFFile = true;
 -            continue;
 -          }
 -        }
 -        if (st.countTokens() > 1 && st.countTokens() < 4)
 -        {
 -          GFFFile = false;
 -          type = st.nextToken();
 -          if (type.equalsIgnoreCase("startgroup"))
 -          {
 -            featureGroup = st.nextToken();
 -            if (st.hasMoreElements())
 -            {
 -              groupLink = st.nextToken();
 -              featureLink.put(featureGroup, groupLink);
 -            }
 -          }
 -          else if (type.equalsIgnoreCase("endgroup"))
 -          {
 -            // We should check whether this is the current group,
 -            // but at present theres no way of showing more than 1 group
 -            st.nextToken();
 -            featureGroup = null;
 -            groupLink = null;
 -          }
 -          else
 -          {
 -            Object colour = null;
 -            String colscheme = st.nextToken();
 -            if (colscheme.indexOf("|") > -1
 -                    || colscheme.trim().equalsIgnoreCase("label"))
 -            {
 -              // Parse '|' separated graduated colourscheme fields:
 -              // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
 -              // can either provide 'label' only, first is optional, next two
 -              // colors are required (but may be
 -              // left blank), next is optional, nxt two min/max are required.
 -              // first is either 'label'
 -              // first/second and third are both hexadecimal or word equivalent
 -              // colour.
 -              // next two are values parsed as floats.
 -              // fifth is either 'above','below', or 'none'.
 -              // sixth is a float value and only required when fifth is either
 -              // 'above' or 'below'.
 -              StringTokenizer gcol = new StringTokenizer(colscheme, "|",
 -                      true);
 -              // set defaults
 -              int threshtype = AnnotationColourGradient.NO_THRESHOLD;
 -              float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
 -              boolean labelCol = false;
 -              // Parse spec line
 -              String mincol = gcol.nextToken();
 -              if (mincol == "|")
 -              {
 -                System.err
 -                        .println("Expected either 'label' or a colour specification in the line: "
 -                                + line);
 -                continue;
 -              }
 -              String maxcol = null;
 -              if (mincol.toLowerCase().indexOf("label") == 0)
 -              {
 -                labelCol = true;
 -                mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
 -                                                                           // '|'
 -                mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
 -              }
 -              String abso = null, minval, maxval;
 -              if (mincol != null)
 -              {
 -                // at least four more tokens
 -                if (mincol.equals("|"))
 -                {
 -                  mincol = "";
 -                }
 -                else
 -                {
 -                  gcol.nextToken(); // skip next '|'
 -                }
 -                // continue parsing rest of line
 -                maxcol = gcol.nextToken();
 -                if (maxcol.equals("|"))
 -                {
 -                  maxcol = "";
 -                }
 -                else
 -                {
 -                  gcol.nextToken(); // skip next '|'
 -                }
 -                abso = gcol.nextToken();
 -                gcol.nextToken(); // skip next '|'
 -                if (abso.toLowerCase().indexOf("abso") != 0)
 -                {
 -                  minval = abso;
 -                  abso = null;
 -                }
 -                else
 -                {
 -                  minval = gcol.nextToken();
 -                  gcol.nextToken(); // skip next '|'
 -                }
 -                maxval = gcol.nextToken();
 -                if (gcol.hasMoreTokens())
 -                {
 -                  gcol.nextToken(); // skip next '|'
 -                }
 -                try
 -                {
 -                  if (minval.length() > 0)
 -                  {
 -                    min = new Float(minval).floatValue();
 -                  }
 -                } catch (Exception e)
 -                {
 -                  System.err
 -                          .println("Couldn't parse the minimum value for graduated colour for type ("
 -                                  + colscheme
 -                                  + ") - did you misspell 'auto' for the optional automatic colour switch ?");
 -                  e.printStackTrace();
 -                }
 -                try
 -                {
 -                  if (maxval.length() > 0)
 -                  {
 -                    max = new Float(maxval).floatValue();
 -                  }
 -                } catch (Exception e)
 -                {
 -                  System.err
 -                          .println("Couldn't parse the maximum value for graduated colour for type ("
 -                                  + colscheme + ")");
 -                  e.printStackTrace();
 -                }
 -              }
 -              else
 -              {
 -                // add in some dummy min/max colours for the label-only
 -                // colourscheme.
 -                mincol = "FFFFFF";
 -                maxcol = "000000";
 -              }
 -              try
 -              {
 -                colour = new jalview.schemes.GraduatedColor(
 -                        new UserColourScheme(mincol).findColour('A'),
 -                        new UserColourScheme(maxcol).findColour('A'), min,
 -                        max);
 -              } catch (Exception e)
 -              {
 -                System.err
 -                        .println("Couldn't parse the graduated colour scheme ("
 -                                + colscheme + ")");
 -                e.printStackTrace();
 -              }
 -              if (colour != null)
 -              {
 -                ((jalview.schemes.GraduatedColor) colour)
 -                        .setColourByLabel(labelCol);
 -                ((jalview.schemes.GraduatedColor) colour)
 -                        .setAutoScaled(abso == null);
 -                // add in any additional parameters
 -                String ttype = null, tval = null;
 -                if (gcol.hasMoreTokens())
 -                {
 -                  // threshold type and possibly a threshold value
 -                  ttype = gcol.nextToken();
 -                  if (ttype.toLowerCase().startsWith("below"))
 -                  {
 -                    ((jalview.schemes.GraduatedColor) colour)
 -                            .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
 -                  }
 -                  else if (ttype.toLowerCase().startsWith("above"))
 -                  {
 -                    ((jalview.schemes.GraduatedColor) colour)
 -                            .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
 -                  }
 -                  else
 -                  {
 -                    ((jalview.schemes.GraduatedColor) colour)
 -                            .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
 -                    if (!ttype.toLowerCase().startsWith("no"))
 -                    {
 -                      System.err
 -                              .println("Ignoring unrecognised threshold type : "
 -                                      + ttype);
 -                    }
 -                  }
 -                }
 -                if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 -                {
 -                  try
 -                  {
 -                    gcol.nextToken();
 -                    tval = gcol.nextToken();
 -                    ((jalview.schemes.GraduatedColor) colour)
 -                            .setThresh(new Float(tval).floatValue());
 -                  } catch (Exception e)
 -                  {
 -                    System.err
 -                            .println("Couldn't parse threshold value as a float: ("
 -                                    + tval + ")");
 -                    e.printStackTrace();
 -                  }
 -                }
 -                // parse the thresh-is-min token ?
 -                if (gcol.hasMoreTokens())
 -                {
 -                  System.err
 -                          .println("Ignoring additional tokens in parameters in graduated colour specification\n");
 -                  while (gcol.hasMoreTokens())
 -                  {
 -                    System.err.println("|" + gcol.nextToken());
 -                  }
 -                  System.err.println("\n");
 -                }
 -              }
 -            }
 -            else
 -            {
 -              UserColourScheme ucs = new UserColourScheme(colscheme);
 -              colour = ucs.findColour('A');
 -            }
 -            if (colour != null)
 -            {
 -              colours.put(type, colour);
 -            }
 -            if (st.hasMoreElements())
 -            {
 -              String link = st.nextToken();
 -              typeLink.put(type, link);
 -              if (featureLink == null)
 -              {
 -                featureLink = new Hashtable();
 -              }
 -              featureLink.put(type, link);
 -            }
 -          }
 -          continue;
 -        }
 -        String seqId = "";
 -        while (st.hasMoreElements())
 -        {
 -
 -          if (GFFFile)
 -          {
 -            // Still possible this is an old Jalview file,
 -            // which does not have type colours at the beginning
 -            seqId = token = st.nextToken();
 -            seq = findName(align, seqId, relaxedIdmatching);
 -            if (seq != null)
 -            {
 -              desc = st.nextToken();
 -              String group = null;
 -              if (doGffSource && desc.indexOf(' ') == -1)
 -              {
 -                // could also be a source term rather than description line
 -                group = new String(desc);
 -              }
 -              type = st.nextToken();
 -              try
 -              {
 -                String stt = st.nextToken();
 -                if (stt.length() == 0 || stt.equals("-"))
 -                {
 -                  start = 0;
 -                }
 -                else
 -                {
 -                  start = Integer.parseInt(stt);
 -                }
 -              } catch (NumberFormatException ex)
 -              {
 -                start = 0;
 -              }
 -              try
 -              {
 -                String stt = st.nextToken();
 -                if (stt.length() == 0 || stt.equals("-"))
 -                {
 -                  end = 0;
 -                }
 -                else
 -                {
 -                  end = Integer.parseInt(stt);
 -                }
 -              } catch (NumberFormatException ex)
 -              {
 -                end = 0;
 -              }
 -              // TODO: decide if non positional feature assertion for input data
 -              // where end==0 is generally valid
 -              if (end == 0)
 -              {
 -                // treat as non-positional feature, regardless.
 -                start = 0;
 -              }
 -              try
 -              {
 -                score = new Float(st.nextToken()).floatValue();
 -              } catch (NumberFormatException ex)
 -              {
 -                score = 0;
 -              }
 -
 -              sf = new SequenceFeature(type, desc, start, end, score, group);
 -
 -              try
 -              {
 -                sf.setValue("STRAND", st.nextToken());
 -                sf.setValue("FRAME", st.nextToken());
 -              } catch (Exception ex)
 -              {
 -              }
 -
 -              if (st.hasMoreTokens())
 -              {
 -                StringBuffer attributes = new StringBuffer();
 -                while (st.hasMoreTokens())
 -                {
 -                  attributes.append("\t" + st.nextElement());
 -                }
 -                // TODO validate and split GFF2 attributes field ? parse out
 -                // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as
 -                // sf.setValue(attrib, val);
 -                sf.setValue("ATTRIBUTES", attributes.toString());
 -              }
 -
 -              seq.addSequenceFeature(sf);
 -              while ((seq = align.findName(seq, seqId, true)) != null)
 -              {
 -                seq.addSequenceFeature(new SequenceFeature(sf));
 -              }
 -              break;
 -            }
 -          }
 -
 -          if (GFFFile && seq == null)
 -          {
 -            desc = token;
 -          }
 -          else
 -          {
 -            desc = st.nextToken();
 -          }
 -          if (!st.hasMoreTokens())
 -          {
 -            System.err
 -                    .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
 -            // in all probability, this isn't a file we understand, so bail
 -            // quietly.
 -            return false;
 -          }
 -
 -          token = st.nextToken();
 -
 -          if (!token.equals("ID_NOT_SPECIFIED"))
 -          {
 -            seq = findName(align, seqId = token, relaxedIdmatching);
 -            st.nextToken();
 -          }
 -          else
 -          {
 -            seqId = null;
 -            try
 -            {
 -              index = Integer.parseInt(st.nextToken());
 -              seq = align.getSequenceAt(index);
 -            } catch (NumberFormatException ex)
 -            {
 -              seq = null;
 -            }
 -          }
 -
 -          if (seq == null)
 -          {
 -            System.out.println("Sequence not found: " + line);
 -            break;
 -          }
 -
 -          start = Integer.parseInt(st.nextToken());
 -          end = Integer.parseInt(st.nextToken());
 -
 -          type = st.nextToken();
 -
 -          if (!colours.containsKey(type))
 -          {
 -            // Probably the old style groups file
 -            UserColourScheme ucs = new UserColourScheme(type);
 -            colours.put(type, ucs.findColour('A'));
 -          }
 -          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 -          if (st.hasMoreTokens())
 -          {
 -            try
 -            {
 -              score = new Float(st.nextToken()).floatValue();
 -              // update colourgradient bounds if allowed to
 -            } catch (NumberFormatException ex)
 -            {
 -              score = 0;
 -            }
 -            sf.setScore(score);
 -          }
 -          if (groupLink != null && removeHTML)
 -          {
 -            sf.addLink(groupLink);
 -            sf.description += "%LINK%";
 -          }
 -          if (typeLink.containsKey(type) && removeHTML)
 -          {
 -            sf.addLink(typeLink.get(type).toString());
 -            sf.description += "%LINK%";
 -          }
 -
 -          parseDescriptionHTML(sf, removeHTML);
 -
 -          seq.addSequenceFeature(sf);
 -
 -          while (seqId != null
 -                  && (seq = align.findName(seq, seqId, false)) != null)
 -          {
 -            seq.addSequenceFeature(new SequenceFeature(sf));
 -          }
 -          // If we got here, its not a GFFFile
 -          GFFFile = false;
 -        }
 -      }
 -      resetMatcher();
 -    } catch (Exception ex)
 -    {
 -      System.out.println(line);
 -      System.out.println("Error parsing feature file: " + ex + "\n" + line);
 -      ex.printStackTrace(System.err);
 -      resetMatcher();
 -      return false;
 -    }
 -
 -    return true;
 -  }
 -
 -  private AlignmentI lastmatchedAl = null;
 -
 -  private SequenceIdMatcher matcher = null;
 -
 -  /**
 -   * clear any temporary handles used to speed up ID matching
 -   */
 -  private void resetMatcher()
 -  {
 -    lastmatchedAl = null;
 -    matcher = null;
 -  }
 -
 -  private SequenceI findName(AlignmentI align, String seqId,
 -          boolean relaxedIdMatching)
 -  {
 -    SequenceI match = null;
 -    if (relaxedIdMatching)
 -    {
 -      if (lastmatchedAl != align)
 -      {
 -        matcher = new SequenceIdMatcher(
 -                (lastmatchedAl = align).getSequencesArray());
 -      }
 -      match = matcher.findIdMatch(seqId);
 -    }
 -    else
 -    {
 -      match = align.findName(seqId, true);
 -    }
 -    return match;
 -  }
 -
 -  public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
 -  {
 -    if (sf.getDescription() == null)
 -    {
 -      return;
 -    }
 -    jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(
 -            sf.getDescription(), removeHTML, newline);
 -
 -    sf.description = (removeHTML) ? parsed.getNonHtmlContent()
 -            : sf.description;
 -    for (String link : parsed.getLinks())
 -    {
 -      sf.addLink(link);
 -    }
 -
 -  }
 -
 -  /**
 -   * generate a features file for seqs includes non-pos features by default.
 -   * 
 -   * @param seqs
 -   *          source of sequence features
 -   * @param visible
 -   *          hash of feature types and colours
 -   * @return features file contents
 -   */
 -  public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
 -  {
 -    return printJalviewFormat(seqs, visible, true, true);
 -  }
 -
 -  /**
 -   * generate a features file for seqs with colours from visible (if any)
 -   * 
 -   * @param seqs
 -   *          source of features
 -   * @param visible
 -   *          hash of Colours for each feature type
 -   * @param visOnly
 -   *          when true only feature types in 'visible' will be output
 -   * @param nonpos
 -   *          indicates if non-positional features should be output (regardless
 -   *          of group or type)
 -   * @return features file contents
 -   */
 -  public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
 -          boolean visOnly, boolean nonpos)
 -  {
 -    StringBuffer out = new StringBuffer();
 -    SequenceFeature[] next;
 -    boolean featuresGen = false;
 -    if (visOnly && !nonpos && (visible == null || visible.size() < 1))
 -    {
 -      // no point continuing.
 -      return "No Features Visible";
 -    }
 -
 -    if (visible != null && visOnly)
 -    {
 -      // write feature colours only if we're given them and we are generating
 -      // viewed features
 -      // TODO: decide if feature links should also be written here ?
 -      Enumeration en = visible.keys();
 -      String type, color;
 -      while (en.hasMoreElements())
 -      {
 -        type = en.nextElement().toString();
 -
 -        if (visible.get(type) instanceof GraduatedColor)
 -        {
 -          GraduatedColor gc = (GraduatedColor) visible.get(type);
 -          color = (gc.isColourByLabel() ? "label|" : "")
 -                  + Format.getHexString(gc.getMinColor()) + "|"
 -                  + Format.getHexString(gc.getMaxColor())
 -                  + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
 -                  + gc.getMax() + "|";
 -          if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 -          {
 -            if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
 -            {
 -              color += "below";
 -            }
 -            else
 -            {
 -              if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
 -              {
 -                System.err.println("WARNING: Unsupported threshold type ("
 -                        + gc.getThreshType() + ") : Assuming 'above'");
 -              }
 -              color += "above";
 -            }
 -            // add the value
 -            color += "|" + gc.getThresh();
 -          }
 -          else
 -          {
 -            color += "none";
 -          }
 -        }
 -        else if (visible.get(type) instanceof java.awt.Color)
 -        {
 -          color = Format.getHexString((java.awt.Color) visible.get(type));
 -        }
 -        else
 -        {
 -          // legacy support for integer objects containing colour triplet values
 -          color = Format.getHexString(new java.awt.Color(Integer
 -                  .parseInt(visible.get(type).toString())));
 -        }
 -        out.append(type);
 -        out.append("\t");
 -        out.append(color);
 -        out.append(newline);
 -      }
 -    }
 -    // Work out which groups are both present and visible
 -    Vector groups = new Vector();
 -    int groupIndex = 0;
 -    boolean isnonpos = false;
 -
 -    for (int i = 0; i < seqs.length; i++)
 -    {
 -      next = seqs[i].getSequenceFeatures();
 -      if (next != null)
 -      {
 -        for (int j = 0; j < next.length; j++)
 -        {
 -          isnonpos = next[j].begin == 0 && next[j].end == 0;
 -          if ((!nonpos && isnonpos)
 -                  || (!isnonpos && visOnly && !visible
 -                          .containsKey(next[j].type)))
 -          {
 -            continue;
 -          }
 -
 -          if (next[j].featureGroup != null
 -                  && !groups.contains(next[j].featureGroup))
 -          {
 -            groups.addElement(next[j].featureGroup);
 -          }
 -        }
 -      }
 -    }
 -
 -    String group = null;
 -    do
 -    {
 -
 -      if (groups.size() > 0 && groupIndex < groups.size())
 -      {
 -        group = groups.elementAt(groupIndex).toString();
 -        out.append(newline);
 -        out.append("STARTGROUP\t");
 -        out.append(group);
 -        out.append(newline);
 -      }
 -      else
 -      {
 -        group = null;
 -      }
 -
 -      for (int i = 0; i < seqs.length; i++)
 -      {
 -        next = seqs[i].getSequenceFeatures();
 -        if (next != null)
 -        {
 -          for (int j = 0; j < next.length; j++)
 -          {
 -            isnonpos = next[j].begin == 0 && next[j].end == 0;
 -            if ((!nonpos && isnonpos)
 -                    || (!isnonpos && visOnly && !visible
 -                            .containsKey(next[j].type)))
 -            {
 -              // skip if feature is nonpos and we ignore them or if we only
 -              // output visible and it isn't non-pos and it's not visible
 -              continue;
 -            }
 -
 -            if (group != null
 -                    && (next[j].featureGroup == null || !next[j].featureGroup
 -                            .equals(group)))
 -            {
 -              continue;
 -            }
 -
 -            if (group == null && next[j].featureGroup != null)
 -            {
 -              continue;
 -            }
 -            // we have features to output
 -            featuresGen = true;
 -            if (next[j].description == null
 -                    || next[j].description.equals(""))
 -            {
 -              out.append(next[j].type + "\t");
 -            }
 -            else
 -            {
 -              if (next[j].links != null
 -                      && next[j].getDescription().indexOf("<html>") == -1)
 -              {
 -                out.append("<html>");
 -              }
 -
 -              out.append(next[j].description + " ");
 -              if (next[j].links != null)
 -              {
 -                for (int l = 0; l < next[j].links.size(); l++)
 -                {
 -                  String label = next[j].links.elementAt(l).toString();
 -                  String href = label.substring(label.indexOf("|") + 1);
 -                  label = label.substring(0, label.indexOf("|"));
 -
 -                  if (next[j].description.indexOf(href) == -1)
 -                  {
 -                    out.append("<a href=\"" + href + "\">" + label + "</a>");
 -                  }
 -                }
 -
 -                if (next[j].getDescription().indexOf("</html>") == -1)
 -                {
 -                  out.append("</html>");
 -                }
 -              }
 -
 -              out.append("\t");
 -            }
 -            out.append(seqs[i].getName());
 -            out.append("\t-1\t");
 -            out.append(next[j].begin);
 -            out.append("\t");
 -            out.append(next[j].end);
 -            out.append("\t");
 -            out.append(next[j].type);
 -            if (next[j].score != Float.NaN)
 -            {
 -              out.append("\t");
 -              out.append(next[j].score);
 -            }
 -            out.append(newline);
 -          }
 -        }
 -      }
 -
 -      if (group != null)
 -      {
 -        out.append("ENDGROUP\t");
 -        out.append(group);
 -        out.append(newline);
 -        groupIndex++;
 -      }
 -      else
 -      {
 -        break;
 -      }
 -
 -    } while (groupIndex < groups.size() + 1);
 -
 -    if (!featuresGen)
 -    {
 -      return "No Features Visible";
 -    }
 -
 -    return out.toString();
 -  }
 -
 -  /**
 -   * generate a gff file for sequence features includes non-pos features by
 -   * default.
 -   * 
 -   * @param seqs
 -   * @param visible
 -   * @return
 -   */
 -  public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
 -  {
 -    return printGFFFormat(seqs, visible, true, true);
 -  }
 -
 -  public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
 -          boolean visOnly, boolean nonpos)
 -  {
 -    StringBuffer out = new StringBuffer();
 -    SequenceFeature[] next;
 -    String source;
 -    boolean isnonpos;
 -    for (int i = 0; i < seqs.length; i++)
 -    {
 -      if (seqs[i].getSequenceFeatures() != null)
 -      {
 -        next = seqs[i].getSequenceFeatures();
 -        for (int j = 0; j < next.length; j++)
 -        {
 -          isnonpos = next[j].begin == 0 && next[j].end == 0;
 -          if ((!nonpos && isnonpos)
 -                  || (!isnonpos && visOnly && !visible
 -                          .containsKey(next[j].type)))
 -          {
 -            continue;
 -          }
 -
 -          source = next[j].featureGroup;
 -          if (source == null)
 -          {
 -            source = next[j].getDescription();
 -          }
 -
 -          out.append(seqs[i].getName());
 -          out.append("\t");
 -          out.append(source);
 -          out.append("\t");
 -          out.append(next[j].type);
 -          out.append("\t");
 -          out.append(next[j].begin);
 -          out.append("\t");
 -          out.append(next[j].end);
 -          out.append("\t");
 -          out.append(next[j].score);
 -          out.append("\t");
 -
 -          if (next[j].getValue("STRAND") != null)
 -          {
 -            out.append(next[j].getValue("STRAND"));
 -            out.append("\t");
 -          }
 -          else
 -          {
 -            out.append(".\t");
 -          }
 -
 -          if (next[j].getValue("FRAME") != null)
 -          {
 -            out.append(next[j].getValue("FRAME"));
 -          }
 -          else
 -          {
 -            out.append(".");
 -          }
 -          // TODO: verify/check GFF - should there be a /t here before attribute
 -          // output ?
 -
 -          if (next[j].getValue("ATTRIBUTES") != null)
 -          {
 -            out.append(next[j].getValue("ATTRIBUTES"));
 -          }
 -
 -          out.append(newline);
 -
 -        }
 -      }
 -    }
 -
 -    return out.toString();
 -  }
 -
 -  /**
 -   * this is only for the benefit of object polymorphism - method does nothing.
 -   */
 -  public void parse()
 -  {
 -    // IGNORED
 -  }
 -
 -  /**
 -   * this is only for the benefit of object polymorphism - method does nothing.
 -   * 
 -   * @return error message
 -   */
 -  public String print()
 -  {
 -    return "USE printGFFFormat() or printJalviewFormat()";
 -  }
 -
 -}
 +package jalview.io;
 +
 +import java.io.*;
 +import java.util.*;
 +
 +import javax.xml.parsers.ParserConfigurationException;
 +
 +import org.xml.sax.SAXException;
 +
 +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 +
 +import jalview.analysis.SequenceIdMatcher;
 +import jalview.datamodel.*;
 +import jalview.schemes.*;
 +import jalview.util.Format;
 +
 +/**
 + * Parse and create Jalview Features files Detects GFF format features files and
 + * parses. Does not implement standard print() - call specific printFeatures or
 + * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object
 + * for the features annotation - this normally works on an exact match.
 + * 
 + * @author AMW
 + * @version $Revision$
 + */
 +public class FeaturesFile extends AlignFile
 +{
 +  /**
 +   * work around for GFF interpretation bug where source string becomes
 +   * description rather than a group
 +   */
 +  private boolean doGffSource = true;
 +
 +  /**
 +   * Creates a new FeaturesFile object.
 +   */
 +  public FeaturesFile()
 +  {
 +  }
 +
 +  /**
 +   * Creates a new FeaturesFile object.
 +   * 
 +   * @param inFile
 +   *          DOCUMENT ME!
 +   * @param type
 +   *          DOCUMENT ME!
 +   * 
 +   * @throws IOException
 +   *           DOCUMENT ME!
 + * @throws SAXException 
 + * @throws ParserConfigurationException 
 + * @throws ExceptionFileFormatOrSyntax 
 + * @throws ExceptionLoadingFailed 
 + * @throws ExceptionPermissionDenied 
 + * @throws InterruptedException 
 + * @throws ExceptionUnmatchedClosingParentheses 
 +   */
 +  public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
 +  {
 +    super(inFile, type);
 +  }
 +
 +  public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
 +  {
 +    super(source);
 +  }
 +
 +  /**
 +   * Parse GFF or sequence features file using case-independent matching, discarding URLs
 +   * @param align - alignment/dataset containing sequences that are to be annotated
 +   * @param colours - hashtable to store feature colour definitions
 +   * @param removeHTML - process html strings into plain text
 +   * @return true if features were added
 +   */
 +  public boolean parse(AlignmentI align, Hashtable colours,
 +          boolean removeHTML)
 +  {
 +    return parse(align, colours, null, removeHTML, false);
 +  }
 +
 +  /**
 +   * Parse GFF or sequence features file optionally using case-independent matching, discarding URLs
 +   * @param align - alignment/dataset containing sequences that are to be annotated
 +   * @param colours - hashtable to store feature colour definitions
 +   * @param removeHTML - process html strings into plain text
 +   * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed
 +   * @return true if features were added
 +   */
 +  public boolean parse(AlignmentI align, 
 +          Map colours, boolean removeHTML, boolean relaxedIdMatching)
 +  {
 +    return parse(align, colours, null, removeHTML, relaxedIdMatching);
 +  }
 +
 +  /**
 +   * Parse GFF or sequence features file optionally using case-independent matching
 +   * @param align - alignment/dataset containing sequences that are to be annotated
 +   * @param colours - hashtable to store feature colour definitions
 +   * @param featureLink - hashtable to store associated URLs 
 +   * @param removeHTML - process html strings into plain text
 +   * @return true if features were added
 +   */
 +  public boolean parse(AlignmentI align, Map colours,
 +          Map featureLink, boolean removeHTML)
 +  {
 +    return parse(align, colours, featureLink, removeHTML, false);
 +  }
 +
 +  /**
 +  /**
 +   * Parse GFF or sequence features file 
 +   * @param align - alignment/dataset containing sequences that are to be annotated
 +   * @param colours - hashtable to store feature colour definitions
 +   * @param featureLink - hashtable to store associated URLs 
 +   * @param removeHTML - process html strings into plain text
 +   * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed
 +   * @return true if features were added
 +   */
 +  public boolean parse(AlignmentI align,
 +          Map colours, Map featureLink, boolean removeHTML, boolean relaxedIdmatching)
 +  {
 +
 +    String line = null;
 +    try
 +    {
 +      SequenceI seq = null;
 +      String type, desc, token = null;
 +
 +      int index, start, end;
 +      float score;
 +      StringTokenizer st;
 +      SequenceFeature sf;
 +      String featureGroup = null, groupLink = null;
 +      Map typeLink = new Hashtable();
 +      /**
 +       * when true, assume GFF style features rather than Jalview style.
 +       */
 +      boolean GFFFile = true;
 +      while ((line = nextLine()) != null)
 +      {
 +        if (line.startsWith("#"))
 +        {
 +          continue;
 +        }
 +
 +        st = new StringTokenizer(line, "\t");
 +        if (st.countTokens() == 1)
 +        {
 +          if (line.trim().equalsIgnoreCase("GFF"))
 +          {
 +            // Start parsing file as if it might be GFF again.
 +            GFFFile = true;
 +            continue;
 +          }
 +        }
 +        if (st.countTokens() > 1 && st.countTokens() < 4)
 +        {
 +          GFFFile = false;
 +          type = st.nextToken();
 +          if (type.equalsIgnoreCase("startgroup"))
 +          {
 +            featureGroup = st.nextToken();
 +            if (st.hasMoreElements())
 +            {
 +              groupLink = st.nextToken();
 +              featureLink.put(featureGroup, groupLink);
 +            }
 +          }
 +          else if (type.equalsIgnoreCase("endgroup"))
 +          {
 +            // We should check whether this is the current group,
 +            // but at present theres no way of showing more than 1 group
 +            st.nextToken();
 +            featureGroup = null;
 +            groupLink = null;
 +          }
 +          else
 +          {
 +            Object colour = null;
 +            String colscheme = st.nextToken();
 +            if (colscheme.indexOf("|") > -1
 +                    || colscheme.trim().equalsIgnoreCase("label"))
 +            {
 +              // Parse '|' separated graduated colourscheme fields:
 +              // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
 +              // can either provide 'label' only, first is optional, next two
 +              // colors are required (but may be
 +              // left blank), next is optional, nxt two min/max are required.
 +              // first is either 'label'
 +              // first/second and third are both hexadecimal or word equivalent
 +              // colour.
 +              // next two are values parsed as floats.
 +              // fifth is either 'above','below', or 'none'.
 +              // sixth is a float value and only required when fifth is either
 +              // 'above' or 'below'.
 +              StringTokenizer gcol = new StringTokenizer(colscheme, "|",
 +                      true);
 +              // set defaults
 +              int threshtype = AnnotationColourGradient.NO_THRESHOLD;
 +              float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
 +              boolean labelCol = false;
 +              // Parse spec line
 +              String mincol = gcol.nextToken();
 +              if (mincol == "|")
 +              {
 +                System.err
 +                        .println("Expected either 'label' or a colour specification in the line: "
 +                                + line);
 +                continue;
 +              }
 +              String maxcol = null;
 +              if (mincol.toLowerCase().indexOf("label") == 0)
 +              {
 +                labelCol = true;
 +                mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
 +                                                                           // '|'
 +                mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
 +              }
 +              String abso = null, minval, maxval;
 +              if (mincol != null)
 +              {
 +                // at least four more tokens
 +                if (mincol.equals("|"))
 +                {
 +                  mincol = "";
 +                }
 +                else
 +                {
 +                  gcol.nextToken(); // skip next '|'
 +                }
 +                // continue parsing rest of line
 +                maxcol = gcol.nextToken();
 +                if (maxcol.equals("|"))
 +                {
 +                  maxcol = "";
 +                }
 +                else
 +                {
 +                  gcol.nextToken(); // skip next '|'
 +                }
 +                abso = gcol.nextToken();
 +                gcol.nextToken(); // skip next '|'
 +                if (abso.toLowerCase().indexOf("abso") != 0)
 +                {
 +                  minval = abso;
 +                  abso = null;
 +                }
 +                else
 +                {
 +                  minval = gcol.nextToken();
 +                  gcol.nextToken(); // skip next '|'
 +                }
 +                maxval = gcol.nextToken();
 +                if (gcol.hasMoreTokens())
 +                {
 +                  gcol.nextToken(); // skip next '|'
 +                }
 +                try
 +                {
 +                  if (minval.length() > 0)
 +                  {
 +                    min = new Float(minval).floatValue();
 +                  }
 +                } catch (Exception e)
 +                {
 +                  System.err
 +                          .println("Couldn't parse the minimum value for graduated colour for type ("
 +                                  + colscheme
 +                                  + ") - did you misspell 'auto' for the optional automatic colour switch ?");
 +                  e.printStackTrace();
 +                }
 +                try
 +                {
 +                  if (maxval.length() > 0)
 +                  {
 +                    max = new Float(maxval).floatValue();
 +                  }
 +                } catch (Exception e)
 +                {
 +                  System.err
 +                          .println("Couldn't parse the maximum value for graduated colour for type ("
 +                                  + colscheme + ")");
 +                  e.printStackTrace();
 +                }
 +              }
 +              else
 +              {
 +                // add in some dummy min/max colours for the label-only
 +                // colourscheme.
 +                mincol = "FFFFFF";
 +                maxcol = "000000";
 +              }
 +              try
 +              {
 +                colour = new jalview.schemes.GraduatedColor(
 +                        new UserColourScheme(mincol).findColour('A'),
 +                        new UserColourScheme(maxcol).findColour('A'), min,
 +                        max);
 +              } catch (Exception e)
 +              {
 +                System.err
 +                        .println("Couldn't parse the graduated colour scheme ("
 +                                + colscheme + ")");
 +                e.printStackTrace();
 +              }
 +              if (colour != null)
 +              {
 +                ((jalview.schemes.GraduatedColor) colour)
 +                        .setColourByLabel(labelCol);
 +                ((jalview.schemes.GraduatedColor) colour)
 +                        .setAutoScaled(abso == null);
 +                // add in any additional parameters
 +                String ttype = null, tval = null;
 +                if (gcol.hasMoreTokens())
 +                {
 +                  // threshold type and possibly a threshold value
 +                  ttype = gcol.nextToken();
 +                  if (ttype.toLowerCase().startsWith("below"))
 +                  {
 +                    ((jalview.schemes.GraduatedColor) colour)
 +                            .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
 +                  }
 +                  else if (ttype.toLowerCase().startsWith("above"))
 +                  {
 +                    ((jalview.schemes.GraduatedColor) colour)
 +                            .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
 +                  }
 +                  else
 +                  {
 +                    ((jalview.schemes.GraduatedColor) colour)
 +                            .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
 +                    if (!ttype.toLowerCase().startsWith("no"))
 +                    {
 +                      System.err
 +                              .println("Ignoring unrecognised threshold type : "
 +                                      + ttype);
 +                    }
 +                  }
 +                }
 +                if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 +                {
 +                  try
 +                  {
 +                    gcol.nextToken();
 +                    tval = gcol.nextToken();
 +                    ((jalview.schemes.GraduatedColor) colour)
 +                            .setThresh(new Float(tval).floatValue());
 +                  } catch (Exception e)
 +                  {
 +                    System.err
 +                            .println("Couldn't parse threshold value as a float: ("
 +                                    + tval + ")");
 +                    e.printStackTrace();
 +                  }
 +                }
 +                // parse the thresh-is-min token ?
 +                if (gcol.hasMoreTokens())
 +                {
 +                  System.err
 +                          .println("Ignoring additional tokens in parameters in graduated colour specification\n");
 +                  while (gcol.hasMoreTokens())
 +                  {
 +                    System.err.println("|" + gcol.nextToken());
 +                  }
 +                  System.err.println("\n");
 +                }
 +              }
 +            }
 +            else
 +            {
 +              UserColourScheme ucs = new UserColourScheme(colscheme);
 +              colour = ucs.findColour('A');
 +            }
 +            if (colour != null)
 +            {
 +              colours.put(type, colour);
 +            }
 +            if (st.hasMoreElements())
 +            {
 +              String link = st.nextToken();
 +              typeLink.put(type, link);
 +              if (featureLink == null)
 +              {
 +                featureLink = new Hashtable();
 +              }
 +              featureLink.put(type, link);
 +            }
 +          }
 +          continue;
 +        }
 +        String seqId = "";
 +        while (st.hasMoreElements())
 +        {
 +
 +          if (GFFFile)
 +          {
 +            // Still possible this is an old Jalview file,
 +            // which does not have type colours at the beginning
 +            seqId = token = st.nextToken();
 +            seq = findName(align, seqId, relaxedIdmatching);
 +            if (seq != null)
 +            {
 +              desc = st.nextToken();
 +              String group = null;
 +              if (doGffSource && desc.indexOf(' ') == -1)
 +              {
 +                // could also be a source term rather than description line
 +                group = new String(desc);
 +              }
 +              type = st.nextToken();
 +              try
 +              {
 +                String stt = st.nextToken();
 +                if (stt.length() == 0 || stt.equals("-"))
 +                {
 +                  start = 0;
 +                }
 +                else
 +                {
 +                  start = Integer.parseInt(stt);
 +                }
 +              } catch (NumberFormatException ex)
 +              {
 +                start = 0;
 +              }
 +              try
 +              {
 +                String stt = st.nextToken();
 +                if (stt.length() == 0 || stt.equals("-"))
 +                {
 +                  end = 0;
 +                }
 +                else
 +                {
 +                  end = Integer.parseInt(stt);
 +                }
 +              } catch (NumberFormatException ex)
 +              {
 +                end = 0;
 +              }
 +              // TODO: decide if non positional feature assertion for input data
 +              // where end==0 is generally valid
 +              if (end == 0)
 +              {
 +                // treat as non-positional feature, regardless.
 +                start = 0;
 +              }
 +              try
 +              {
 +                score = new Float(st.nextToken()).floatValue();
 +              } catch (NumberFormatException ex)
 +              {
 +                score = 0;
 +              }
 +
 +              sf = new SequenceFeature(type, desc, start, end, score, group);
 +
 +              try
 +              {
 +                sf.setValue("STRAND", st.nextToken());
 +                sf.setValue("FRAME", st.nextToken());
 +              } catch (Exception ex)
 +              {
 +              }
 +
 +              if (st.hasMoreTokens())
 +              {
 +                StringBuffer attributes = new StringBuffer();
 +                while (st.hasMoreTokens())
 +                {
 +                  attributes.append("\t" + st.nextElement());
 +                }
 +                // TODO validate and split GFF2 attributes field ? parse out
 +                // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as
 +                // sf.setValue(attrib, val);
 +                sf.setValue("ATTRIBUTES", attributes.toString());
 +              }
 +
 +              seq.addSequenceFeature(sf);
 +              while ((seq = align.findName(seq, seqId, true)) != null)
 +              {
 +                seq.addSequenceFeature(new SequenceFeature(sf));
 +              }
 +              break;
 +            }
 +          }
 +
 +          if (GFFFile && seq == null)
 +          {
 +            desc = token;
 +          }
 +          else
 +          {
 +            desc = st.nextToken();
 +          }
 +          if (!st.hasMoreTokens())
 +          {
 +            System.err
 +                    .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
 +            // in all probability, this isn't a file we understand, so bail
 +            // quietly.
 +            return false;
 +          }
 +
 +          token = st.nextToken();
 +
 +          if (!token.equals("ID_NOT_SPECIFIED"))
 +          {
 +            seq = findName(align, seqId = token, relaxedIdmatching);
 +            st.nextToken();
 +          }
 +          else
 +          {
 +            seqId = null;
 +            try
 +            {
 +              index = Integer.parseInt(st.nextToken());
 +              seq = align.getSequenceAt(index);
 +            } catch (NumberFormatException ex)
 +            {
 +              seq = null;
 +            }
 +          }
 +
 +          if (seq == null)
 +          {
 +            System.out.println("Sequence not found: " + line);
 +            break;
 +          }
 +
 +          start = Integer.parseInt(st.nextToken());
 +          end = Integer.parseInt(st.nextToken());
 +
 +          type = st.nextToken();
 +
 +          if (!colours.containsKey(type))
 +          {
 +            // Probably the old style groups file
 +            UserColourScheme ucs = new UserColourScheme(type);
 +            colours.put(type, ucs.findColour('A'));
 +          }
 +          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 +          if (st.hasMoreTokens())
 +          {
 +            try
 +            {
 +              score = new Float(st.nextToken()).floatValue();
 +              // update colourgradient bounds if allowed to
 +            } catch (NumberFormatException ex)
 +            {
 +              score = 0;
 +            }
 +            sf.setScore(score);
 +          }
 +          if (groupLink != null && removeHTML)
 +          {
 +            sf.addLink(groupLink);
 +            sf.description += "%LINK%";
 +          }
 +          if (typeLink.containsKey(type) && removeHTML)
 +          {
 +            sf.addLink(typeLink.get(type).toString());
 +            sf.description += "%LINK%";
 +          }
 +
 +          parseDescriptionHTML(sf, removeHTML);
 +
 +          seq.addSequenceFeature(sf);
 +
 +          while (seqId != null
 +                  && (seq = align.findName(seq, seqId, false)) != null)
 +          {
 +            seq.addSequenceFeature(new SequenceFeature(sf));
 +          }
 +          // If we got here, its not a GFFFile
 +          GFFFile = false;
 +        }
 +      }
 +      resetMatcher();
 +    } catch (Exception ex)
 +    {
 +      System.out.println(line);
 +      System.out.println("Error parsing feature file: " + ex + "\n" + line);
 +      ex.printStackTrace(System.err);
 +      resetMatcher();
 +      return false;
 +    }
 +
 +    return true;
 +  }
 +
 +  private AlignmentI lastmatchedAl = null;
 +
 +  private SequenceIdMatcher matcher = null;
 +
 +  /**
 +   * clear any temporary handles used to speed up ID matching
 +   */
 +  private void resetMatcher()
 +  {
 +    lastmatchedAl = null;
 +    matcher = null;
 +  }
 +
 +  private SequenceI findName(AlignmentI align, String seqId,
 +          boolean relaxedIdMatching)
 +  {
 +    SequenceI match = null;
 +    if (relaxedIdMatching)
 +    {
 +      if (lastmatchedAl != align)
 +      {
 +        matcher = new SequenceIdMatcher(
 +                (lastmatchedAl = align).getSequencesArray());
 +      }
 +      match = matcher.findIdMatch(seqId);
 +    }
 +    else
 +    {
 +      match = align.findName(seqId, true);
 +    }
 +    return match;
 +  }
 +
 +  public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
 +  {
 +    if (sf.getDescription() == null)
 +    {
 +      return;
 +    }
 +    jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(sf.getDescription(), removeHTML, newline);
 +
 +    sf.description = (removeHTML) ? parsed.getNonHtmlContent() : sf.description;
 +    for (String link:parsed.getLinks())
 +    {
 +      sf.addLink(link);
 +    }
 +
 +  }
 +
 +  /**
 +   * generate a features file for seqs includes non-pos features by default.
 +   * 
 +   * @param seqs
 +   *          source of sequence features
 +   * @param visible
 +   *          hash of feature types and colours
 +   * @return features file contents
 +   */
 +  public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
 +  {
 +    return printJalviewFormat(seqs, visible, true, true);
 +  }
 +
 +  /**
 +   * generate a features file for seqs with colours from visible (if any)
 +   * 
 +   * @param seqs
 +   *          source of features
 +   * @param visible
 +   *          hash of Colours for each feature type
 +   * @param visOnly
 +   *          when true only feature types in 'visible' will be output
 +   * @param nonpos
 +   *          indicates if non-positional features should be output (regardless
 +   *          of group or type)
 +   * @return features file contents
 +   */
 +  public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
 +          boolean visOnly, boolean nonpos)
 +  {
 +    StringBuffer out = new StringBuffer();
 +    SequenceFeature[] next;
 +    boolean featuresGen = false;
 +    if (visOnly && !nonpos && (visible == null || visible.size() < 1))
 +    {
 +      // no point continuing.
 +      return "No Features Visible";
 +    }
 +
 +    if (visible != null && visOnly)
 +    {
 +      // write feature colours only if we're given them and we are generating
 +      // viewed features
 +      // TODO: decide if feature links should also be written here ?
 +      Enumeration en = visible.keys();
 +      String type, color;
 +      while (en.hasMoreElements())
 +      {
 +        type = en.nextElement().toString();
 +
 +        if (visible.get(type) instanceof GraduatedColor)
 +        {
 +          GraduatedColor gc = (GraduatedColor) visible.get(type);
 +          color = (gc.isColourByLabel() ? "label|" : "")
 +                  + Format.getHexString(gc.getMinColor()) + "|"
 +                  + Format.getHexString(gc.getMaxColor())
 +                  + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
 +                  + gc.getMax() + "|";
 +          if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 +          {
 +            if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
 +            {
 +              color += "below";
 +            }
 +            else
 +            {
 +              if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
 +              {
 +                System.err.println("WARNING: Unsupported threshold type ("
 +                        + gc.getThreshType() + ") : Assuming 'above'");
 +              }
 +              color += "above";
 +            }
 +            // add the value
 +            color += "|" + gc.getThresh();
 +          }
 +          else
 +          {
 +            color += "none";
 +          }
 +        }
 +        else if (visible.get(type) instanceof java.awt.Color)
 +        {
 +          color = Format.getHexString((java.awt.Color) visible.get(type));
 +        }
 +        else
 +        {
 +          // legacy support for integer objects containing colour triplet values
 +          color = Format.getHexString(new java.awt.Color(Integer
 +                  .parseInt(visible.get(type).toString())));
 +        }
 +        out.append(type);
 +        out.append("\t");
 +        out.append(color);
 +        out.append(newline);
 +      }
 +    }
 +    // Work out which groups are both present and visible
 +    Vector groups = new Vector();
 +    int groupIndex = 0;
 +    boolean isnonpos = false;
 +
 +    for (int i = 0; i < seqs.length; i++)
 +    {
 +      next = seqs[i].getSequenceFeatures();
 +      if (next != null)
 +      {
 +        for (int j = 0; j < next.length; j++)
 +        {
 +          isnonpos = next[j].begin == 0 && next[j].end == 0;
 +          if ((!nonpos && isnonpos)
 +                  || (!isnonpos && visOnly && !visible
 +                          .containsKey(next[j].type)))
 +          {
 +            continue;
 +          }
 +
 +          if (next[j].featureGroup != null
 +                  && !groups.contains(next[j].featureGroup))
 +          {
 +            groups.addElement(next[j].featureGroup);
 +          }
 +        }
 +      }
 +    }
 +
 +    String group = null;
 +    do
 +    {
 +
 +      if (groups.size() > 0 && groupIndex < groups.size())
 +      {
 +        group = groups.elementAt(groupIndex).toString();
 +        out.append(newline);
 +        out.append("STARTGROUP\t");
 +        out.append(group);
 +        out.append(newline);
 +      }
 +      else
 +      {
 +        group = null;
 +      }
 +
 +      for (int i = 0; i < seqs.length; i++)
 +      {
 +        next = seqs[i].getSequenceFeatures();
 +        if (next != null)
 +        {
 +          for (int j = 0; j < next.length; j++)
 +          {
 +            isnonpos = next[j].begin == 0 && next[j].end == 0;
 +            if ((!nonpos && isnonpos)
 +                    || (!isnonpos && visOnly && !visible
 +                            .containsKey(next[j].type)))
 +            {
 +              // skip if feature is nonpos and we ignore them or if we only
 +              // output visible and it isn't non-pos and it's not visible
 +              continue;
 +            }
 +
 +            if (group != null
 +                    && (next[j].featureGroup == null || !next[j].featureGroup
 +                            .equals(group)))
 +            {
 +              continue;
 +            }
 +
 +            if (group == null && next[j].featureGroup != null)
 +            {
 +              continue;
 +            }
 +            // we have features to output
 +            featuresGen = true;
 +            if (next[j].description == null
 +                    || next[j].description.equals(""))
 +            {
 +              out.append(next[j].type + "\t");
 +            }
 +            else
 +            {
 +              if (next[j].links != null
 +                      && next[j].getDescription().indexOf("<html>") == -1)
 +              {
 +                out.append("<html>");
 +              }
 +
 +              out.append(next[j].description + " ");
 +              if (next[j].links != null)
 +              {
 +                for (int l = 0; l < next[j].links.size(); l++)
 +                {
 +                  String label = next[j].links.elementAt(l).toString();
 +                  String href = label.substring(label.indexOf("|") + 1);
 +                  label = label.substring(0, label.indexOf("|"));
 +
 +                  if (next[j].description.indexOf(href) == -1)
 +                  {
 +                    out.append("<a href=\"" + href + "\">" + label + "</a>");
 +                  }
 +                }
 +
 +                if (next[j].getDescription().indexOf("</html>") == -1)
 +                {
 +                  out.append("</html>");
 +                }
 +              }
 +
 +              out.append("\t");
 +            }
 +            out.append(seqs[i].getName());
 +            out.append("\t-1\t");
 +            out.append(next[j].begin);
 +            out.append("\t");
 +            out.append(next[j].end);
 +            out.append("\t");
 +            out.append(next[j].type);
 +            if (next[j].score != Float.NaN)
 +            {
 +              out.append("\t");
 +              out.append(next[j].score);
 +            }
 +            out.append(newline);
 +          }
 +        }
 +      }
 +
 +      if (group != null)
 +      {
 +        out.append("ENDGROUP\t");
 +        out.append(group);
 +        out.append(newline);
 +        groupIndex++;
 +      }
 +      else
 +      {
 +        break;
 +      }
 +
 +    } while (groupIndex < groups.size() + 1);
 +
 +    if (!featuresGen)
 +    {
 +      return "No Features Visible";
 +    }
 +
 +    return out.toString();
 +  }
 +
 +  /**
 +   * generate a gff file for sequence features includes non-pos features by
 +   * default.
 +   * 
 +   * @param seqs
 +   * @param visible
 +   * @return
 +   */
 +  public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
 +  {
 +    return printGFFFormat(seqs, visible, true, true);
 +  }
 +
 +  public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
 +          boolean visOnly, boolean nonpos)
 +  {
 +    StringBuffer out = new StringBuffer();
 +    SequenceFeature[] next;
 +    String source;
 +    boolean isnonpos;
 +    for (int i = 0; i < seqs.length; i++)
 +    {
 +      if (seqs[i].getSequenceFeatures() != null)
 +      {
 +        next = seqs[i].getSequenceFeatures();
 +        for (int j = 0; j < next.length; j++)
 +        {
 +          isnonpos = next[j].begin == 0 && next[j].end == 0;
 +          if ((!nonpos && isnonpos)
 +                  || (!isnonpos && visOnly && !visible
 +                          .containsKey(next[j].type)))
 +          {
 +            continue;
 +          }
 +
 +          source = next[j].featureGroup;
 +          if (source == null)
 +          {
 +            source = next[j].getDescription();
 +          }
 +
 +          out.append(seqs[i].getName());
 +          out.append("\t");
 +          out.append(source);
 +          out.append("\t");
 +          out.append(next[j].type);
 +          out.append("\t");
 +          out.append(next[j].begin);
 +          out.append("\t");
 +          out.append(next[j].end);
 +          out.append("\t");
 +          out.append(next[j].score);
 +          out.append("\t");
 +
 +          if (next[j].getValue("STRAND") != null)
 +          {
 +            out.append(next[j].getValue("STRAND"));
 +            out.append("\t");
 +          }
 +          else
 +          {
 +            out.append(".\t");
 +          }
 +
 +          if (next[j].getValue("FRAME") != null)
 +          {
 +            out.append(next[j].getValue("FRAME"));
 +          }
 +          else
 +          {
 +            out.append(".");
 +          }
 +          // TODO: verify/check GFF - should there be a /t here before attribute
 +          // output ?
 +
 +          if (next[j].getValue("ATTRIBUTES") != null)
 +          {
 +            out.append(next[j].getValue("ATTRIBUTES"));
 +          }
 +
 +          out.append(newline);
 +
 +        }
 +      }
 +    }
 +
 +    return out.toString();
 +  }
 +
 +  /**
 +   * this is only for the benefit of object polymorphism - method does nothing.
 +   */
 +  public void parse()
 +  {
 +    // IGNORED
 +  }
 +
 +  /**
 +   * this is only for the benefit of object polymorphism - method does nothing.
 +   * 
 +   * @return error message
 +   */
 +  public String print()
 +  {
 +    return "USE printGFFFormat() or printJalviewFormat()";
 +  }
 +
 +}
diff --cc src/jalview/io/SimpleBlastFile.java
index 5c2b2f3,5cbf78d..9256283
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@@ -20,17 -20,7 +20,16 @@@ package jalview.io
  import java.io.*;
  import java.util.*;
  
 +import javax.xml.parsers.ParserConfigurationException;
 +
 +import org.xml.sax.SAXException;
 +
 +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 +
  import jalview.datamodel.*;
- import jalview.util.*;
  
  /**
   * parse a simple blast report. Attempt to cope with query anchored and pairwise
diff --cc src/jalview/io/StockholmFile.java
index 77e29bb,669181a..07a5c80
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@@ -1,749 -1,688 +1,749 @@@
 -/*
 - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
 - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 - * 
 - * This file is part of Jalview.
 - * 
 - * Jalview is free software: you can redistribute it and/or
 - * modify it under the terms of the GNU General Public License 
 - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 - *  
 - * Jalview is distributed in the hope that it will be useful, but 
 - * WITHOUT ANY WARRANTY; without even the implied warranty 
 - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 - * PURPOSE.  See the GNU General Public License for more details.
 - * 
 - * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 - */
 -/*
 - * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
 - */
 -package jalview.io;
 -
 -import java.io.*;
 -import java.util.*;
 -
 -import com.stevesoft.pat.*;
 -import jalview.datamodel.*;
 -
 -// import org.apache.log4j.*;
 -
 -/**
 - * This class is supposed to parse a Stockholm format file into Jalview There
 - * are TODOs in this class: we do not know what the database source and version
 - * is for the file when parsing the #GS= AC tag which associates accessions with
 - * sequences. Database references are also not parsed correctly: a separate
 - * reference string parser must be added to parse the database reference form
 - * into Jalview's local representation.
 - * 
 - * @author bsb at sanger.ac.uk
 - * @version 0.3 + jalview mods
 - * 
 - */
 -public class StockholmFile extends AlignFile
 -{
 -  // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
 -
 -  public StockholmFile()
 -  {
 -  }
 -
 -  public StockholmFile(String inFile, String type) throws IOException
 -  {
 -    super(inFile, type);
 -  }
 -
 -  public StockholmFile(FileParse source) throws IOException
 -  {
 -    super(source);
 -  }
 -
 -  public void initData()
 -  {
 -    super.initData();
 -  }
 -
 -  /**
 -   * Parse a file in Stockholm format into Jalview's data model. The file has to
 -   * be passed at construction time
 -   * 
 -   * @throws IOException
 -   *           If there is an error with the input file
 -   */
 -  public void parse() throws IOException
 -  {
 -    StringBuffer treeString = new StringBuffer();
 -    String treeName = null;
 -    // --------------- Variable Definitions -------------------
 -    String line;
 -    String version;
 -    // String id;
 -    Hashtable seqAnn = new Hashtable(); // Sequence related annotations
 -    Hashtable seqs = new Hashtable();
 -    Regex p, r, rend, s, x;
 -
 -    // Temporary line for processing RNA annotation
 -    // String RNAannot = "";
 -
 -    // ------------------ Parsing File ----------------------
 -    // First, we have to check that this file has STOCKHOLM format, i.e. the
 -    // first line must match
 -    r = new Regex("# STOCKHOLM ([\\d\\.]+)");
 -    if (!r.search(nextLine()))
 -    {
 -      throw new IOException(
 -              "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
 -    }
 -    else
 -    {
 -      version = r.stringMatched(1);
 -      // logger.debug("Stockholm version: " + version);
 -    }
 -
 -    // We define some Regexes here that will be used regularily later
 -    rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
 -    p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
 -    // id/from/to
 -    s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
 -    r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
 -    x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
 -
 -    // Convert all bracket types to parentheses (necessary for passing to VARNA)
 -    Regex openparen = new Regex("(<|\\[)", "(");
 -    Regex closeparen = new Regex("(>|\\])", ")");
 -
 -    // Detect if file is RNA by looking for bracket types
 -    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
 -
 -    rend.optimize();
 -    p.optimize();
 -    s.optimize();
 -    r.optimize();
 -    x.optimize();
 -    openparen.optimize();
 -    closeparen.optimize();
 -
 -    while ((line = nextLine()) != null)
 -    {
 -      if (line.length() == 0)
 -      {
 -        continue;
 -      }
 -      if (rend.search(line))
 -      {
 -        // End of the alignment, pass stuff back
 -
 -        this.noSeqs = seqs.size();
 -        // logger.debug("Number of sequences: " + this.noSeqs);
 -        Enumeration accs = seqs.keys();
 -        while (accs.hasMoreElements())
 -        {
 -          String acc = (String) accs.nextElement();
 -          // logger.debug("Processing sequence " + acc);
 -          String seq = (String) seqs.remove(acc);
 -          if (maxLength < seq.length())
 -          {
 -            maxLength = seq.length();
 -          }
 -          int start = 1;
 -          int end = -1;
 -          String sid = acc;
 -          /*
 -           * Retrieve hash of annotations for this accession Associate
 -           * Annotation with accession
 -           */
 -          Hashtable accAnnotations = null;
 -
 -          if (seqAnn != null && seqAnn.containsKey(acc))
 -          {
 -            accAnnotations = (Hashtable) seqAnn.remove(acc);
 -            // TODO: add structures to sequence
 -          }
 -
 -          // Split accession in id and from/to
 -          if (p.search(acc))
 -          {
 -            sid = p.stringMatched(1);
 -            start = Integer.parseInt(p.stringMatched(2));
 -            end = Integer.parseInt(p.stringMatched(3));
 -          }
 -          // logger.debug(sid + ", " + start + ", " + end);
 -
 -          Sequence seqO = new Sequence(sid, seq, start, end);
 -          // Add Description (if any)
 -          if (accAnnotations != null && accAnnotations.containsKey("DE"))
 -          {
 -            String desc = (String) accAnnotations.get("DE");
 -            seqO.setDescription((desc == null) ? "" : desc);
 -          }
 -          // Add DB References (if any)
 -          if (accAnnotations != null && accAnnotations.containsKey("DR"))
 -          {
 -            String dbr = (String) accAnnotations.get("DR");
 -            if (dbr != null && dbr.indexOf(";") > -1)
 -            {
 -              String src = dbr.substring(0, dbr.indexOf(";"));
 -              String acn = dbr.substring(dbr.indexOf(";") + 1);
 -              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
 -              // seqO.addDBRef(dbref);
 -            }
 -          }
 -          if (accAnnotations != null && accAnnotations.containsKey("SS"))
 -          {
 -            Vector v = (Vector) accAnnotations.get("SS");
 -
 -            for (int i = 0; i < v.size(); i++)
 -            {
 -              AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);
 -              seqO.addAlignmentAnnotation(an);
 -              // annotations.add(an);
 -            }
 -          }
 -
 -          Hashtable features = null;
 -          // We need to adjust the positions of all features to account for gaps
 -          try
 -          {
 -            features = (Hashtable) accAnnotations.remove("features");
 -          } catch (java.lang.NullPointerException e)
 -          {
 -            // loggerwarn("Getting Features for " + acc + ": " +
 -            // e.getMessage());
 -            // continue;
 -          }
 -          // if we have features
 -          if (features != null)
 -          {
 -            int posmap[] = seqO.findPositionMap();
 -            Enumeration i = features.keys();
 -            while (i.hasMoreElements())
 -            {
 -              // TODO: parse out secondary structure annotation as annotation
 -              // row
 -              // TODO: parse out scores as annotation row
 -              // TODO: map coding region to core jalview feature types
 -              String type = i.nextElement().toString();
 -              Hashtable content = (Hashtable) features.remove(type);
 -              Enumeration j = content.keys();
 -              while (j.hasMoreElements())
 -              {
 -                String desc = j.nextElement().toString();
 -                String ns = content.get(desc).toString();
 -                char[] byChar = ns.toCharArray();
 -                for (int k = 0; k < byChar.length; k++)
 -                {
 -                  char c = byChar[k];
 -                  if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
 -                  // uses
 -                  // '.'
 -                  // for
 -                  // feature
 -                  // background
 -                  {
 -                    int new_pos = posmap[k]; // look up nearest seqeunce
 -                    // position to this column
 -                    SequenceFeature feat = new SequenceFeature(type, desc,
 -                            new_pos, new_pos, 0f, null);
 -
 -                    seqO.addSequenceFeature(feat);
 -                  }
 -                }
 -              }
 -
 -            }
 -
 -          }
 -          // garbage collect
 -
 -          // logger.debug("Adding seq " + acc + " from " + start + " to " + end
 -          // + ": " + seq);
 -          this.seqs.addElement(seqO);
 -        }
 -        return; // finished parsing this segment of source
 -      }
 -      else if (!r.search(line))
 -      {
 -        // System.err.println("Found sequence line: " + line);
 -
 -        // Split sequence in sequence and accession parts
 -        if (!x.search(line))
 -        {
 -          // logger.error("Could not parse sequence line: " + line);
 -          throw new IOException("Could not parse sequence line: " + line);
 -        }
 -        String ns = (String) seqs.get(x.stringMatched(1));
 -        if (ns == null)
 -        {
 -          ns = "";
 -        }
 -        ns += x.stringMatched(2);
 -
 -        seqs.put(x.stringMatched(1), ns);
 -      }
 -      else
 -      {
 -        String annType = r.stringMatched(1);
 -        String annContent = r.stringMatched(2);
 -
 -        // System.err.println("type:" + annType + " content: " + annContent);
 -
 -        if (annType.equals("GF"))
 -        {
 -          /*
 -           * Generic per-File annotation, free text Magic features: #=GF NH
 -           * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
 -           * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
 -           * 
 -           * Compulsory fields: ------------------
 -           * 
 -           * AC Accession number: Accession number in form PFxxxxx.version or
 -           * PBxxxxxx. ID Identification: One word name for family. DE
 -           * Definition: Short description of family. AU Author: Authors of the
 -           * entry. SE Source of seed: The source suggesting the seed members
 -           * belong to one family. GA Gathering method: Search threshold to
 -           * build the full alignment. TC Trusted Cutoff: Lowest sequence score
 -           * and domain score of match in the full alignment. NC Noise Cutoff:
 -           * Highest sequence score and domain score of match not in full
 -           * alignment. TP Type: Type of family -- presently Family, Domain,
 -           * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
 -           * Alignment Method The order ls and fs hits are aligned to the model
 -           * to build the full align. // End of alignment.
 -           * 
 -           * Optional fields: ----------------
 -           * 
 -           * DC Database Comment: Comment about database reference. DR Database
 -           * Reference: Reference to external database. RC Reference Comment:
 -           * Comment about literature reference. RN Reference Number: Reference
 -           * Number. RM Reference Medline: Eight digit medline UI number. RT
 -           * Reference Title: Reference Title. RA Reference Author: Reference
 -           * Author RL Reference Location: Journal location. PI Previous
 -           * identifier: Record of all previous ID lines. KW Keywords: Keywords.
 -           * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
 -           * NL Location: Location of nested domains - sequence ID, start and
 -           * end of insert.
 -           * 
 -           * Obsolete fields: ----------- AL Alignment method of seed: The
 -           * method used to align the seed members.
 -           */
 -          // Let's save the annotations, maybe we'll be able to do something
 -          // with them later...
 -          Regex an = new Regex("(\\w+)\\s*(.*)");
 -          if (an.search(annContent))
 -          {
 -            if (an.stringMatched(1).equals("NH"))
 -            {
 -              treeString.append(an.stringMatched(2));
 -            }
 -            else if (an.stringMatched(1).equals("TN"))
 -            {
 -              if (treeString.length() > 0)
 -              {
 -                if (treeName == null)
 -                {
 -                  treeName = "Tree " + (getTreeCount() + 1);
 -                }
 -                addNewickTree(treeName, treeString.toString());
 -              }
 -              treeName = an.stringMatched(2);
 -              treeString = new StringBuffer();
 -            }
 -            setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
 -          }
 -        }
 -        else if (annType.equals("GS"))
 -        {
 -          // Generic per-Sequence annotation, free text
 -          /*
 -           * Pfam uses these features: Feature Description ---------------------
 -           * ----------- AC <accession> ACcession number DE <freetext>
 -           * DEscription DR <db>; <accession>; Database Reference OS <organism>
 -           * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
 -           * LO <look> Look (Color, etc.)
 -           */
 -          if (s.search(annContent))
 -          {
 -            String acc = s.stringMatched(1);
 -            String type = s.stringMatched(2);
 -            String content = s.stringMatched(3);
 -            // TODO: store DR in a vector.
 -            // TODO: store AC according to generic file db annotation.
 -            Hashtable ann;
 -            if (seqAnn.containsKey(acc))
 -            {
 -              ann = (Hashtable) seqAnn.get(acc);
 -            }
 -            else
 -            {
 -              ann = new Hashtable();
 -            }
 -            ann.put(type, content);
 -            seqAnn.put(acc, ann);
 -          }
 -          else
 -          {
 -            throw new IOException("Error parsing " + line);
 -          }
 -        }
 -        else if (annType.equals("GC"))
 -        {
 -          // Generic per-Column annotation, exactly 1 char per column
 -          // always need a label.
 -          if (x.search(annContent))
 -          {
 -            // parse out and create alignment annotation directly.
 -            parseAnnotationRow(annotations, x.stringMatched(1),
 -                    x.stringMatched(2));
 -          }
 -        }
 -        else if (annType.equals("GR"))
 -        {
 -          // Generic per-Sequence AND per-Column markup, exactly 1 char per
 -          // column
 -          /*
 -           * Feature Description Markup letters ------- -----------
 -           * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
 -           * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
 -           * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
 -           * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
 -           * or after) [0-2]
 -           */
 -          if (s.search(annContent))
 -          {
 -            String acc = s.stringMatched(1);
 -            String type = s.stringMatched(2);
 -            String seq = new String(s.stringMatched(3));
 -            String description = null;
 -            // Check for additional information about the current annotation
 -            // We use a simple string tokenizer here for speed
 -            StringTokenizer sep = new StringTokenizer(seq, " \t");
 -            description = sep.nextToken();
 -            if (sep.hasMoreTokens())
 -            {
 -              seq = sep.nextToken();
 -            }
 -            else
 -            {
 -              seq = description;
 -              description = new String();
 -            }
 -            // sequence id with from-to fields
 -
 -            Hashtable ann;
 -            // Get an object with all the annotations for this sequence
 -            if (seqAnn.containsKey(acc))
 -            {
 -              // logger.debug("Found annotations for " + acc);
 -              ann = (Hashtable) seqAnn.get(acc);
 -            }
 -            else
 -            {
 -              // logger.debug("Creating new annotations holder for " + acc);
 -              ann = new Hashtable();
 -              seqAnn.put(acc, ann);
 -            }
 -            // TODO test structure, call parseAnnotationRow with vector from
 -            // hashtable for specific sequence
 -            Hashtable features;
 -            // Get an object with all the content for an annotation
 -            if (ann.containsKey("features"))
 -            {
 -              // logger.debug("Found features for " + acc);
 -              features = (Hashtable) ann.get("features");
 -            }
 -            else
 -            {
 -              // logger.debug("Creating new features holder for " + acc);
 -              features = new Hashtable();
 -              ann.put("features", features);
 -            }
 -
 -            Hashtable content;
 -            if (features.containsKey(this.id2type(type)))
 -            {
 -              // logger.debug("Found content for " + this.id2type(type));
 -              content = (Hashtable) features.get(this.id2type(type));
 -            }
 -            else
 -            {
 -              // logger.debug("Creating new content holder for " +
 -              // this.id2type(type));
 -              content = new Hashtable();
 -              features.put(this.id2type(type), content);
 -            }
 -            String ns = (String) content.get(description);
 -            if (ns == null)
 -            {
 -              ns = "";
 -            }
 -            ns += seq;
 -            content.put(description, ns);
 -
 -            if (type.equals("SS"))
 -            {
 -              Hashtable strucAnn;
 -              if (seqAnn.containsKey(acc))
 -              {
 -                strucAnn = (Hashtable) seqAnn.get(acc);
 -              }
 -              else
 -              {
 -                strucAnn = new Hashtable();
 -              }
 -
 -              Vector newStruc = new Vector();
 -              parseAnnotationRow(newStruc, type, ns);
 -
 -              strucAnn.put(type, newStruc);
 -              seqAnn.put(acc, strucAnn);
 -            }
 -          }
 -          else
 -          {
 -            System.err
 -                    .println("Warning - couldn't parse sequence annotation row line:\n"
 -                            + line);
 -            // throw new IOException("Error parsing " + line);
 -          }
 -        }
 -        else
 -        {
 -          throw new IOException("Unknown annotation detected: " + annType
 -                  + " " + annContent);
 -        }
 -      }
 -    }
 -    if (treeString.length() > 0)
 -    {
 -      if (treeName == null)
 -      {
 -        treeName = "Tree " + (1 + getTreeCount());
 -      }
 -      addNewickTree(treeName, treeString.toString());
 -    }
 -  }
 -
 -  protected static AlignmentAnnotation parseAnnotationRow(
 -          Vector annotation, String label, String annots)
 -  {
 -    String convert1, convert2 = null;
 -
 -    // Convert all bracket types to parentheses
 -    Regex openparen = new Regex("(<|\\[)", "(");
 -    Regex closeparen = new Regex("(>|\\])", ")");
 -
 -    // Detect if file is RNA by looking for bracket types
 -    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
 -
 -    convert1 = openparen.replaceAll(annots);
 -    convert2 = closeparen.replaceAll(convert1);
 -    annots = convert2;
 -
 -    String type = (label.indexOf("_cons") == label.length() - 5) ? label
 -            .substring(0, label.length() - 5) : label;
 -    boolean ss = false;
 -    type = id2type(type);
 -    if (type.equals("secondary structure"))
 -    {
 -      ss = true;
 -    }
 -    // decide on secondary structure or not.
 -    Annotation[] els = new Annotation[annots.length()];
 -    for (int i = 0; i < annots.length(); i++)
 -    {
 -      String pos = annots.substring(i, i + 1);
 -      Annotation ann;
 -      ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
 -      // be written out
 -      if (ss)
 -      {
 -        if (detectbrackets.search(pos))
 -        {
 -          ann.secondaryStructure = jalview.schemes.ResidueProperties
 -                  .getRNASecStrucState(pos).charAt(0);
 -        }
 -        else
 -        {
 -          ann.secondaryStructure = jalview.schemes.ResidueProperties
 -                  .getDssp3state(pos).charAt(0);
 -        }
 -
 -        if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
 -        {
 -          ann.displayCharacter = ""; // null; // " ";
 -        }
 -        else
 -        {
 -          ann.displayCharacter = " " + ann.displayCharacter;
 -        }
 -      }
 -
 -      els[i] = ann;
 -    }
 -    AlignmentAnnotation annot = null;
 -    Enumeration e = annotation.elements();
 -    while (e.hasMoreElements())
 -    {
 -      annot = (AlignmentAnnotation) e.nextElement();
 -      if (annot.label.equals(type))
 -        break;
 -      annot = null;
 -    }
 -    if (annot == null)
 -    {
 -      annot = new AlignmentAnnotation(type, type, els);
 -      annotation.addElement(annot);
 -    }
 -    else
 -    {
 -      Annotation[] anns = new Annotation[annot.annotations.length
 -              + els.length];
 -      System.arraycopy(annot.annotations, 0, anns, 0,
 -              annot.annotations.length);
 -      System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
 -      annot.annotations = anns;
 -      // System.out.println("else: ");
 -    }
 -    return annot;
 -  }
 -
 -  public static String print(SequenceI[] s)
 -  {
 -    return "not yet implemented";
 -  }
 -
 -  public String print()
 -  {
 -    return print(getSeqsAsArray());
 -  }
 -
 -  private static Hashtable typeIds = null;
 -  static
 -  {
 -    if (typeIds == null)
 -    {
 -      typeIds = new Hashtable();
 -      typeIds.put("SS", "secondary structure");
 -      typeIds.put("SA", "surface accessibility");
 -      typeIds.put("TM", "transmembrane");
 -      typeIds.put("PP", "posterior probability");
 -      typeIds.put("LI", "ligand binding");
 -      typeIds.put("AS", "active site");
 -      typeIds.put("IN", "intron");
 -      typeIds.put("IR", "interacting residue");
 -      typeIds.put("AC", "accession");
 -      typeIds.put("OS", "organism");
 -      typeIds.put("CL", "class");
 -      typeIds.put("DE", "description");
 -      typeIds.put("DR", "reference");
 -      typeIds.put("LO", "look");
 -      typeIds.put("RF", "reference positions");
 -
 -    }
 -  }
 -
 -  protected static String id2type(String id)
 -  {
 -    if (typeIds.containsKey(id))
 -    {
 -      return (String) typeIds.get(id);
 -    }
 -    System.err.println("Warning : Unknown Stockholm annotation type code "
 -            + id);
 -    return id;
 -  }
 -  /**
 -   * //ssline is complete secondary structure line private AlignmentAnnotation
 -   * addHelices(Vector annotation, String label, String ssline) {
 -   * 
 -   * // decide on secondary structure or not. Annotation[] els = new
 -   * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {
 -   * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new
 -   * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
 -   * 
 -   * ann.secondaryStructure =
 -   * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);
 -   * 
 -   * ann.displayCharacter = "x" + ann.displayCharacter;
 -   * 
 -   * System.out.println(ann.displayCharacter);
 -   * 
 -   * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =
 -   * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =
 -   * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))
 -   * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =
 -   * new AlignmentAnnotation(type, type, els);
 -   * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new
 -   * Annotation[helicesAnnot.annotations.length + els.length];
 -   * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,
 -   * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,
 -   * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =
 -   * anns; }
 -   * 
 -   * helicesAnnot.features = Rna.GetBasePairs(ssline);
 -   * Rna.HelixMap(helicesAnnot.features);
 -   * 
 -   * 
 -   * return helicesAnnot; }
 -   */
 -}
 +/*
-  * 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
++ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
++ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 + * 
 + * This file is part of Jalview.
 + * 
 + * Jalview is free software: you can redistribute it and/or
 + * modify it under the terms of the GNU General Public License 
 + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-  * 
++ *  
 + * Jalview is distributed in the hope that it will be useful, but 
 + * WITHOUT ANY WARRANTY; without even the implied warranty 
 + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 + * PURPOSE.  See the GNU General Public License for more details.
 + * 
 + * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 + */
 +/*
 + * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
 + */
 +package jalview.io;
 +
 +import java.io.*;
 +import java.util.*;
 +
 +import javax.xml.parsers.ParserConfigurationException;
 +
 +import org.xml.sax.SAXException;
 +
 +import com.stevesoft.pat.*;
 +
 +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 +import fr.orsay.lri.varna.factories.RNAFactory;
 +import fr.orsay.lri.varna.models.rna.RNA;
 +import jalview.datamodel.*;
 +import jalview.analysis.Rna;
 +
 +// import org.apache.log4j.*;
 +
 +/**
 + * This class is supposed to parse a Stockholm format file into Jalview There
 + * are TODOs in this class: we do not know what the database source and version
 + * is for the file when parsing the #GS= AC tag which associates accessions with
 + * sequences. Database references are also not parsed correctly: a separate
 + * reference string parser must be added to parse the database reference form
 + * into Jalview's local representation.
 + * 
 + * @author bsb at sanger.ac.uk
 + * @version 0.3 + jalview mods
 + * 
 + */
 +public class StockholmFile extends AlignFile
 +{
 +  // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
 +  protected ArrayList<RNA> result;
 +  public String id;
 +  
 +  public StockholmFile()
 +  {
 +  }
 +
 +  public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
 +  {
 +    super(inFile, type);
 +  }
 +
 +  public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
 +  {
 +    super(source);
 +  }
 +
 +  public void initData()
 +  {
 +    super.initData();
 +  }
 +
 +  /**
 +   * Parse a file in Stockholm format into Jalview's data model. The file has to
 +   * be passed at construction time
 +   * 
 +   * @throws IOException
 +   *           If there is an error with the input file
 + * @throws ExceptionUnmatchedClosingParentheses 
 +   */
 +  public void parse() throws IOException, ExceptionUnmatchedClosingParentheses
 +  {
 +	  FileReader fr = null;
 +	  fr = new FileReader(inFile); 
 +
 +	BufferedReader r = new BufferedReader (fr);
 +	result = RNAFactory.loadSecStrStockholm(r);
 +	System.out.println("this is the secondary scructure:" +result.size());
 +	SequenceI[] seqs = new SequenceI[result.size()];
 +	  System.out.println(type); //the type is "File"
 +	  System.out.println(inFile );//inFile is the path
 +	for(int i=0;i<result.size();i++)
 +	{
 +		RNA current = result.get(i);
 +	
 +		  System.out.println(current.getSeq());
 +		  //System.out.println(result.get(i).getStructBPSEQ());
 +		  System.out.println(result.get(i).getStructDBN(true));
 +		  System.out.println(i);
 +		String rna =current.getStructDBN(true);
 +		 String seq = current.getSeq();
 +		 int begin=0;
 +		  int end = seq.length()-1;
 +		  id = safeName(getDataName());
 +		  seqs[i] = new Sequence(id, seq, begin, end);
 +		  String[] annot=new String[rna.length()] ;
 +		  Annotation[] ann = new Annotation[rna.length()];
 +		  for(int j=0;j<rna.length();j++)
 +			{
 +			  annot[j] =rna.substring(j,j+1);
 +		  
 +			}
 +		  
 +		  for(int k=0;k<rna.length();k++)
 +		{
 +			  ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);
 +			  			  
 +		}
 +		  AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);
 +		  
 +		  seqs[i].addAlignmentAnnotation(align);
 +		  seqs[i].setRNA(result.get(i));
 +		  this.annotations.addElement(align);
 +		}
 + 	  this.setSeqs(seqs);
 +	
 +  }
 +//    r = new Regex("# STOCKHOLM ([\\d\\.]+)");
 + //    if (!r.search(nextLine()))
 +//    {
 +//      throw new IOException(
 +//              "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
 +//    }
 +//    else
 +//    {
 +//      version = r.stringMatched(1);
 +//      // logger.debug("Stockholm version: " + version);
 +//    }
 +//
 +//    // We define some Regexes here that will be used regularily later
 +//    rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
 +//    p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
 +//    // id/from/to
 +//    s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
 +//    r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
 +//    x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
 +//
 +//    // Convert all bracket types to parentheses (necessary for passing to VARNA)
 +//    Regex openparen = new Regex("(<|\\[)", "(");
 +//    Regex closeparen = new Regex("(>|\\])", ")");
 +//
 +//    // Detect if file is RNA by looking for bracket types
 +//    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
 +//
 +//    rend.optimize();
 +//    p.optimize();
 +//    s.optimize();
 +//    r.optimize();
 +//    x.optimize();
 +//    openparen.optimize();
 +//    closeparen.optimize();
 +//
 +//    while ((line = nextLine()) != null)
 +//    {
 +//      if (line.length() == 0)
 +//      {
 +//        continue;
 +//      }
 +//      if (rend.search(line))
 +//      {
 +//        // End of the alignment, pass stuff back
 +//
 +//        this.noSeqs = seqs.size();
 +//        // logger.debug("Number of sequences: " + this.noSeqs);
 +//        Enumeration accs = seqs.keys();
 +//        while (accs.hasMoreElements())
 +//        {
 +//          String acc = (String) accs.nextElement();
 +//          // logger.debug("Processing sequence " + acc);
 +//          String seq = (String) seqs.remove(acc);
 +//          if (maxLength < seq.length())
 +//          {
 +//            maxLength = seq.length();
 +//          }
 +//          int start = 1;
 +//          int end = -1;
 +//          String sid = acc;
 +//          /*
 +//           * Retrieve hash of annotations for this accession
 +//           * Associate Annotation with accession
 +//           */
 +//          Hashtable accAnnotations = null;
 +//
 +//          if (seqAnn != null && seqAnn.containsKey(acc))
 +//          {
 +//            accAnnotations = (Hashtable) seqAnn.remove(acc);
 +//            //TODO: add structures to sequence
 +//          }
 +//
 +//          // Split accession in id and from/to
 +//          if (p.search(acc))
 +//          {
 +//            sid = p.stringMatched(1);
 +//            start = Integer.parseInt(p.stringMatched(2));
 +//            end = Integer.parseInt(p.stringMatched(3));
 +//          }
 +//          // logger.debug(sid + ", " + start + ", " + end);
 +//
 +//          Sequence seqO = new Sequence(sid, seq, start, end);
 +//          // Add Description (if any)
 +//          if (accAnnotations != null && accAnnotations.containsKey("DE"))
 +//          {
 +//            String desc = (String) accAnnotations.get("DE");
 +//            seqO.setDescription((desc == null) ? "" : desc);
 +//          }
 +//          // Add DB References (if any)
 +//          if (accAnnotations != null && accAnnotations.containsKey("DR"))
 +//          {
 +//            String dbr = (String) accAnnotations.get("DR");
 +//            if (dbr != null && dbr.indexOf(";") > -1)
 +//            {
 +//              String src = dbr.substring(0, dbr.indexOf(";"));
 +//              String acn = dbr.substring(dbr.indexOf(";") + 1);
 +//              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
 +//              // seqO.addDBRef(dbref);
 +//            }
 +//          }        
 +//          if (accAnnotations != null && accAnnotations.containsKey("SS"))
 +//          {
 +//        	  Vector v = (Vector) accAnnotations.get("SS");
 +//        	  
 +//        	  for (int i = 0; i < v.size(); i++)
 +//        	    {
 +//        		  AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);
 +//        		  seqO.addAlignmentAnnotation(an);
 +//        		  //annotations.add(an);
 +//        	    }
 +//          }
 +//        
 +//          Hashtable features = null;
 +//          // We need to adjust the positions of all features to account for gaps
 +//          try
 +//          {
 +//            features = (Hashtable) accAnnotations.remove("features");
 +//          } catch (java.lang.NullPointerException e)
 +//          {
 +//            // loggerwarn("Getting Features for " + acc + ": " +
 +//            // e.getMessage());
 +//            // continue;
 +//          }
 +//          // if we have features
 +//          if (features != null)
 +//          {
 +//            int posmap[] = seqO.findPositionMap();
 +//            Enumeration i = features.keys();
 +//            while (i.hasMoreElements())
 +//            {
 +//              // TODO: parse out secondary structure annotation as annotation
 +//              // row
 +//              // TODO: parse out scores as annotation row
 +//              // TODO: map coding region to core jalview feature types
 +//              String type = i.nextElement().toString();
 +//              Hashtable content = (Hashtable) features.remove(type);
 +//              Enumeration j = content.keys();
 +//              while (j.hasMoreElements())
 +//              {
 +//                String desc = j.nextElement().toString();
 +//                String ns = content.get(desc).toString();
 +//                char[] byChar = ns.toCharArray();
 +//                for (int k = 0; k < byChar.length; k++)
 +//                {
 +//                  char c = byChar[k];
 +//                  if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
 +//                  // uses
 +//                  // '.'
 +//                  // for
 +//                  // feature
 +//                  // background
 +//                  {
 +//                    int new_pos = posmap[k]; // look up nearest seqeunce
 +//                    // position to this column
 +//                    SequenceFeature feat = new SequenceFeature(type, desc,
 +//                            new_pos, new_pos, 0f, null);
 +//
 +//                    seqO.addSequenceFeature(feat);
 +//                  }
 +//                }
 +//              }
 +//
 +//            }
 +//
 +//          }
 +//          // garbage collect
 +//
 +//          // logger.debug("Adding seq " + acc + " from " + start + " to " + end
 +//          // + ": " + seq);
 +//          this.seqs.addElement(seqO);
 +//        }
 +//        return; // finished parsing this segment of source
 +//      }
 +//      else if (!r.search(line))
 +//      {
 +//        // System.err.println("Found sequence line: " + line);
 +//
 +//        // Split sequence in sequence and accession parts
 +//        if (!x.search(line))
 +//        {
 +//          // logger.error("Could not parse sequence line: " + line);
 +//          throw new IOException("Could not parse sequence line: " + line);
 +//        }
 +//        String ns = (String) seqs.get(x.stringMatched(1));
 +//        if (ns == null)
 +//        {
 +//          ns = "";
 +//        }
 +//        ns += x.stringMatched(2);
 +//
 +//        seqs.put(x.stringMatched(1), ns);
 +//      }
 +//      else
 +//      {
 +//        String annType = r.stringMatched(1);
 +//        String annContent = r.stringMatched(2);
 +//
 +//        // System.err.println("type:" + annType + " content: " + annContent);
 +//
 +//        if (annType.equals("GF"))
 +//        {
 +//          /*
 +//           * Generic per-File annotation, free text Magic features: #=GF NH
 +//           * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
 +//           * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
 +//           * 
 +//           * Compulsory fields: ------------------
 +//           * 
 +//           * AC Accession number: Accession number in form PFxxxxx.version or
 +//           * PBxxxxxx. ID Identification: One word name for family. DE
 +//           * Definition: Short description of family. AU Author: Authors of the
 +//           * entry. SE Source of seed: The source suggesting the seed members
 +//           * belong to one family. GA Gathering method: Search threshold to
 +//           * build the full alignment. TC Trusted Cutoff: Lowest sequence score
 +//           * and domain score of match in the full alignment. NC Noise Cutoff:
 +//           * Highest sequence score and domain score of match not in full
 +//           * alignment. TP Type: Type of family -- presently Family, Domain,
 +//           * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
 +//           * Alignment Method The order ls and fs hits are aligned to the model
 +//           * to build the full align. // End of alignment.
 +//           * 
 +//           * Optional fields: ----------------
 +//           * 
 +//           * DC Database Comment: Comment about database reference. DR Database
 +//           * Reference: Reference to external database. RC Reference Comment:
 +//           * Comment about literature reference. RN Reference Number: Reference
 +//           * Number. RM Reference Medline: Eight digit medline UI number. RT
 +//           * Reference Title: Reference Title. RA Reference Author: Reference
 +//           * Author RL Reference Location: Journal location. PI Previous
 +//           * identifier: Record of all previous ID lines. KW Keywords: Keywords.
 +//           * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
 +//           * NL Location: Location of nested domains - sequence ID, start and
 +//           * end of insert.
 +//           * 
 +//           * Obsolete fields: ----------- AL Alignment method of seed: The
 +//           * method used to align the seed members.
 +//           */
 +//          // Let's save the annotations, maybe we'll be able to do something
 +//          // with them later...
 +//          Regex an = new Regex("(\\w+)\\s*(.*)");
 +//          if (an.search(annContent))
 +//          {
 +//            if (an.stringMatched(1).equals("NH"))
 +//            {
 +//              treeString.append(an.stringMatched(2));
 +//            }
 +//            else if (an.stringMatched(1).equals("TN"))
 +//            {
 +//              if (treeString.length() > 0)
 +//              {
 +//                if (treeName == null)
 +//                {
 +//                  treeName = "Tree " + (getTreeCount() + 1);
 +//                }
 +//                addNewickTree(treeName, treeString.toString());
 +//              }
 +//              treeName = an.stringMatched(2);
 +//              treeString = new StringBuffer();
 +//            }
 +//            setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
 +//          }
 +//        }
 +//        else if (annType.equals("GS"))
 +//        {
 +//          // Generic per-Sequence annotation, free text
 +//          /*
 +//           * Pfam uses these features: Feature Description ---------------------
 +//           * ----------- AC <accession> ACcession number DE <freetext>
 +//           * DEscription DR <db>; <accession>; Database Reference OS <organism>
 +//           * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
 +//           * LO <look> Look (Color, etc.)
 +//           */
 +//          if (s.search(annContent))
 +//          {
 +//            String acc = s.stringMatched(1);
 +//            String type = s.stringMatched(2);
 +//            String content = s.stringMatched(3);
 +//            // TODO: store DR in a vector.
 +//            // TODO: store AC according to generic file db annotation.
 +//            Hashtable ann;
 +//            if (seqAnn.containsKey(acc))
 +//            {
 +//              ann = (Hashtable) seqAnn.get(acc);
 +//            }
 +//            else
 +//            {
 +//              ann = new Hashtable();
 +//            }
 +//            ann.put(type, content);
 +//            seqAnn.put(acc, ann);
 +//          }
 +//          else
 +//          {
 +//            throw new IOException("Error parsing " + line);
 +//          }
 +//        }
 +//        else if (annType.equals("GC"))
 +//        {
 +//          // Generic per-Column annotation, exactly 1 char per column
 +//          // always need a label.
 +//          if (x.search(annContent))
 +//          {
 +//            // parse out and create alignment annotation directly.
 +//            parseAnnotationRow(annotations, x.stringMatched(1),
 +//                    x.stringMatched(2));
 +//          }
 +//        }
 +//        else if (annType.equals("GR"))
 +//        {
 +//          // Generic per-Sequence AND per-Column markup, exactly 1 char per
 +//          // column
 +//          /*
 +//           * Feature Description Markup letters ------- -----------
 +//           * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
 +//           * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
 +//           * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
 +//           * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
 +//           * or after) [0-2]
 +//           */
 +//          if (s.search(annContent))
 +//          {
 +//            String acc = s.stringMatched(1);
 +//            String type = s.stringMatched(2);
 +//            String seq = new String(s.stringMatched(3));
 +//            String description = null;
 +//            // Check for additional information about the current annotation
 +//            // We use a simple string tokenizer here for speed
 +//            StringTokenizer sep = new StringTokenizer(seq, " \t");
 +//            description = sep.nextToken();
 +//            if (sep.hasMoreTokens())
 +//            {
 +//              seq = sep.nextToken();
 +//            }
 +//            else
 +//            {
 +//              seq = description;
 +//              description = new String();
 +//            }
 +//            // sequence id with from-to fields
 +//
 +//            Hashtable ann;
 +//            // Get an object with all the annotations for this sequence
 +//            if (seqAnn.containsKey(acc))
 +//            {
 +//              // logger.debug("Found annotations for " + acc);
 +//              ann = (Hashtable) seqAnn.get(acc);
 +//            }
 +//            else
 +//            {
 +//              // logger.debug("Creating new annotations holder for " + acc);
 +//              ann = new Hashtable();
 +//              seqAnn.put(acc, ann);
 +//            }
 +//            //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence
 +//            Hashtable features;
 +//            // Get an object with all the content for an annotation
 +//            if (ann.containsKey("features"))
 +//            {
 +//              // logger.debug("Found features for " + acc);
 +//              features = (Hashtable) ann.get("features");
 +//            }
 +//            else
 +//            {
 +//              // logger.debug("Creating new features holder for " + acc);
 +//              features = new Hashtable();
 +//              ann.put("features", features);
 +//            }
 +//
 +//            Hashtable content;
 +//            if (features.containsKey(this.id2type(type)))
 +//            {
 +//              // logger.debug("Found content for " + this.id2type(type));
 +//              content = (Hashtable) features.get(this.id2type(type));
 +//            }
 +//            else
 +//            {
 +//              // logger.debug("Creating new content holder for " +
 +//              // this.id2type(type));
 +//              content = new Hashtable();
 +//              features.put(this.id2type(type), content);
 +//            }
 +//            String ns = (String) content.get(description);
 +//            if (ns == null)
 +//            {
 +//              ns = "";
 +//            }
 +//            ns += seq;
 +//            content.put(description, ns);
 +//
 +//            if(type.equals("SS")){
 +//                Hashtable strucAnn;
 +//                if (seqAnn.containsKey(acc))
 +//                {
 +//                  strucAnn = (Hashtable) seqAnn.get(acc);
 +//                }
 +//                else
 +//                {
 +//                  strucAnn = new Hashtable();
 +//                }
 +//                
 +//                Vector newStruc=new Vector();
 +//                parseAnnotationRow(newStruc, type,ns);
 +//                
 +//                strucAnn.put(type, newStruc);
 +//                seqAnn.put(acc, strucAnn);
 +//             }
 +//          }
 +//          else
 +//          {
 +//            System.err
 +//                    .println("Warning - couldn't parse sequence annotation row line:\n"
 +//                            + line);
 +//            // throw new IOException("Error parsing " + line);
 +//          }
 +//        }
 +//        else
 +//        {
 +//          throw new IOException("Unknown annotation detected: " + annType
 +//                  + " " + annContent);
 +//        }
 +//      }
 +//    }
 +//    if (treeString.length() > 0)
 +//    {
 +//      if (treeName == null)
 +//      {
 +//        treeName = "Tree " + (1 + getTreeCount());
 +//      }
 +//      addNewickTree(treeName, treeString.toString());
 +//    }
 +//  }
 +//
 +  protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,
 +          String label, String annots)
 +  {
 +    String convert1, convert2 = null;
 +
 +    // Convert all bracket types to parentheses
 +    Regex openparen = new Regex("(<|\\[)", "(");
 +    Regex closeparen = new Regex("(>|\\])", ")");
 +
 +   // Detect if file is RNA by looking for bracket types
 +    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
 +
 +    convert1 = openparen.replaceAll(annots);
 +    convert2 = closeparen.replaceAll(convert1);
 +    annots = convert2;
 +
 +    String type = (label.indexOf("_cons") == label.length() - 5) ? label
 +            .substring(0, label.length() - 5) : label;
 +    boolean ss = false;
 +    type = id2type(type);
 +    if (type.equals("secondary structure"))
 +    {
 +      ss = true;
 +    }
 +    // decide on secondary structure or not.
 +    Annotation[] els = new Annotation[annots.length()];
 +    for (int i = 0; i < annots.length(); i++)
 +    {
 +      String pos = annots.substring(i, i + 1);
 +      Annotation ann;
 +      ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
 +      // be written out
 +      if (ss)
 +      {
 +        if (detectbrackets.search(pos))
 +        {
 +          ann.secondaryStructure = jalview.schemes.ResidueProperties
 +                 .getRNASecStrucState(pos).charAt(0);
 +        }
 +        else
 +        {
 +          ann.secondaryStructure = jalview.schemes.ResidueProperties
 +                  .getDssp3state(pos).charAt(0);
 +        }
 +
 +        if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
 +        {
 +          ann.displayCharacter = ""; // null; // " ";
 +        }
 +        else
 +       {
 +          ann.displayCharacter = " " + ann.displayCharacter;
 +        }
 +      }
 +
 +      els[i] = ann;
 +    }
 +   AlignmentAnnotation annot = null;
 +    Enumeration e = annotation.elements();
 +    while (e.hasMoreElements())
 +    {
 +      annot = (AlignmentAnnotation) e.nextElement();
 +      if (annot.label.equals(type))
 +        break;
 +      annot = null;
 +    }
 +    if (annot == null)
 +    {
 +      annot = new AlignmentAnnotation(type, type, els);
 +      annotation.addElement(annot);
 +    }
 +    else
 +   {
 +      Annotation[] anns = new Annotation[annot.annotations.length
 +              + els.length];
 +     System.arraycopy(annot.annotations, 0, anns, 0,
 +             annot.annotations.length);
 +      System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
 +      annot.annotations = anns;
 +      //System.out.println("else: ");
 +   }
 +   return annot;
 +  }
 +
 +  public static String print(SequenceI[] s)
 +  {
 +    return "not yet implemented";
 +  }
 +
 +  public String print()
 +  {
 +    return print(getSeqsAsArray());
 +  }
 +
 +  private static Hashtable typeIds = null;
 +  static
 +  {
 +    if (typeIds == null)
 +    {
 +      typeIds = new Hashtable();
 +      typeIds.put("SS", "secondary structure");
 +      typeIds.put("SA", "surface accessibility");
 +      typeIds.put("TM", "transmembrane");
 +      typeIds.put("PP", "posterior probability");
 +      typeIds.put("LI", "ligand binding");
 +      typeIds.put("AS", "active site");
 +      typeIds.put("IN", "intron");
 +      typeIds.put("IR", "interacting residue");
 +      typeIds.put("AC", "accession");
 +      typeIds.put("OS", "organism");
 +      typeIds.put("CL", "class");
 +      typeIds.put("DE", "description");
 +      typeIds.put("DR", "reference");
 +      typeIds.put("LO", "look");
 +      typeIds.put("RF", "reference positions");
 +
 +    }
 +  }
 +
 +  protected static String id2type(String id)
 +  {
 +    if (typeIds.containsKey(id))
 +    {
 +      return (String) typeIds.get(id);
 +    }
 +    System.err.println("Warning : Unknown Stockholm annotation type code "
 +            + id);
 +    return id;
 +  }
 +  /**
 +   * //ssline is complete secondary structure line private AlignmentAnnotation
 +   * addHelices(Vector annotation, String label, String ssline) {
 +   * 
 +   * // decide on secondary structure or not. Annotation[] els = new
 +   * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {
 +   * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new
 +   * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
 +   * 
 +   * ann.secondaryStructure =
 +   * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);
 +   * 
 +   * ann.displayCharacter = "x" + ann.displayCharacter;
 +   * 
 +   * System.out.println(ann.displayCharacter);
 +   * 
 +   * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =
 +   * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =
 +   * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))
 +   * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =
 +   * new AlignmentAnnotation(type, type, els);
 +   * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new
 +   * Annotation[helicesAnnot.annotations.length + els.length];
 +   * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,
 +   * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,
 +   * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =
 +   * anns; }
 +   * 
 +   * helicesAnnot.features = Rna.GetBasePairs(ssline);
 +   * Rna.HelixMap(helicesAnnot.features);
 +   * 
 +   * 
 +   * return helicesAnnot; }
 +   * 
 +   */
 +  /**
 +   * make a friendly ID string.
 +   * 
 +   * @param dataName
 +   * @return truncated dataName to after last '/'
 +   */
 +  private String safeName(String dataName)
 +  {
 +    int b = 0;
 +    while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )
 +    {	    	   
 +    	dataName = dataName.substring(b + 1).trim();
 +    	
 +    }
 +    int e = (dataName.length() - dataName.indexOf("."))+1;
 +    dataName = dataName.substring(1,e).trim();
 +    return dataName;
 +  }
- }
++}
diff --cc src/jalview/io/TCoffeeScoreFile.java
index 9f26670,42a2caa..178caad
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@@ -19,23 -31,14 +31,23 @@@ import java.util.LinkedHashMap
  import java.util.List;
  import java.util.Map;
  
 +import javax.xml.parsers.ParserConfigurationException;
 +
 +import org.xml.sax.SAXException;
 +
 +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 +
  /**
-  * A file parse for T-Coffee score ascii format. This file contains the alignment consensus 
-  * for each resude in any sequence.
+  * A file parse for T-Coffee score ascii format. This file contains the
+  * alignment consensus for each resude in any sequence.
   * <p>
-  * This file is procuded by <code>t_coffee</code> providing the option 
+  * This file is procuded by <code>t_coffee</code> providing the option
   * <code>-output=score_ascii </code> to the program command line
   * 
-  * An example file is the following 
+  * An example file is the following
   * 
   * <pre>
   * T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
@@@ -79,17 -82,18 +91,17 @@@
   * 
   * 
   * @author Paolo Di Tommaso
-  *
+  * 
   */
 -public class TCoffeeScoreFile extends AlignFile
 -{
 -
 -  public TCoffeeScoreFile(String inFile, String type) throws IOException
 +public class TCoffeeScoreFile extends AlignFile {
 +	
 +  public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
    {
      super(inFile, type);
-     
+ 
    }
  
 -  public TCoffeeScoreFile(FileParse source) throws IOException
 +  public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
    {
      super(source);
    }
diff --cc src/jalview/renderer/AnnotationRenderer.java
index a46aa92,7ab7fda..bfe2156
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@@ -794,78 -481,16 +813,82 @@@ public class AnnotationRendere
                  break;
  
                case 'E':
-                 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
-                         column, validRes, validEnd);
+                 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
+                         iconOffset, startRes, column, validRes, validEnd);
                  break;
  
 -              case 'S': // Stem case for RNA secondary structure
 -              case 's': // and opposite direction
 -                drawStemAnnot(g, row_annotations, lastSSX, x, y,
 -                        iconOffset, startRes, column, validRes, validEnd);
 +              case '(': // Stem case for RNA secondary structure
 +              case ')': // and opposite direction
 +                drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
 +                        column, validRes, validEnd);
++//              case 'S': // Stem case for RNA secondary structure
++//              case 's': // and opposite direction
++//                drawStemAnnot(g, row_annotations, lastSSX, x, y,
++//                        iconOffset, startRes, column, validRes, validEnd);
                  break;
 -
 +              case '{':
 +              case '}':
 +              case '[':
 +              case ']':
 +              case '>':
 +              case '<':
 +              case 'A':
 +              case 'a':
 +              case 'B':
 +              case 'b':
 +              case 'C':
 +              case 'c':
 +              case 'D':
 +              case 'd':
 +              case '1':
 +              case 'e':
 +              case 'F':
 +              case 'f':
 +              case 'G':
 +              case 'g':
 +              case '2':
 +              case 'h':
 +              case 'I':
 +              case 'i':
 +              case 'J':
 +              case 'j':
 +              case 'K':
 +              case 'k':
 +              case 'L':
 +              case 'l':
 +              case 'M':
 +              case 'm':
 +              case 'N':
 +              case 'n':
 +              case 'O':
 +              case 'o':
 +              case 'P':
 +              case 'p':
 +              case 'Q':
 +              case 'q':
 +              case 'R':
 +              case 'r':
 +              case 'S':
 +              case 's':
 +              case 'T':
 +              case 't':
 +              case 'U':
 +              case 'u':
 +              case 'V':
 +              case 'v':
 +              case 'W':
 +              case 'w':
 +              case 'X':
 +              case 'x':
 +              case 'Y':
 +              case 'y':
 +              case 'Z':
 +              case 'z':
 +            	  //System.out.println(lastSS);
 +              	  Color nonCanColor= getNotCanonicalColor(lastSS);
 +            	  drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
 +                          column, validRes, validEnd);
 +            	  break;
                default:
                  g.setColor(Color.gray);
                  g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
@@@ -927,73 -552,12 +950,73 @@@
            break;
          case 's':
          case 'S': // Stem case for RNA secondary structure
-           drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
-                   column, validRes, validEnd);
+           drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+                   startRes, column, validRes, validEnd);
            break;
 +        case '{':
 +        case '}':
 +        case '[':
 +        case ']':
 +        case '>':
 +        case '<':
 +        case 'A':
 +        case 'a':
 +        case 'B':
 +        case 'b':
 +        case 'C':
 +        case 'c':
 +        case 'D':
 +        case 'd':
 +        case '1':
 +        case 'e':
 +        case 'F':
 +        case 'f':
 +        case 'G':
 +        case 'g':
 +        case '2':
 +        case 'h':
 +        case 'I':
 +        case 'i':
 +        case 'J':
 +        case 'j':
 +        case 'K':
 +        case 'k':
 +        case 'L':
 +        case 'l':
 +        case 'M':
 +        case 'm':
 +        case 'N':
 +        case 'n':
 +        case 'O':
 +        case 'o':
 +        case 'P':
 +        case 'p':
 +        case 'Q':
 +        case 'q':
 +        case 'R':
 +        case 'r':
 +        case 'T':
 +        case 't':
 +        case 'U':
 +        case 'u':
 +        case 'V':
 +        case 'v':
 +        case 'W':
 +        case 'w':
 +        case 'X':
 +        case 'x':
 +        case 'Y':
 +        case 'y':
 +        case 'Z':
 +        case 'z':
 +        	//System.out.println(lastSS);
 +          Color nonCanColor = getNotCanonicalColor(lastSS);
 +      	  drawNotCanonicalAnnot(g,nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
 +                    column, validRes, validEnd);
 +      	  break;
          default:
-           drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
-                   column, validRes, validEnd);
+           drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
+                   startRes, column, validRes, validEnd);
            break;
          }
        }
@@@ -1070,12 -634,10 +1093,12 @@@
    private final Color HELIX_COLOUR = Color.red;
  
    private final Color STEM_COLOUR = Color.blue;
 +  
 +  private  Color sdNOTCANONICAL_COLOUR;
  
-   public void drawGlyphLine(Graphics g, Annotation[] row,
-           int lastSSX, int x, int y, int iconOffset, int startRes,
-           int column, boolean validRes, boolean validEnd)
+   public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
+           int x, int y, int iconOffset, int startRes, int column,
+           boolean validRes, boolean validEnd)
    {
      g.setColor(GLYPHLINE_COLOR);
      g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
diff --cc src/jalview/schemes/ColourSchemeProperty.java
index fc6d536,47dbde2..4132f32
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@@ -346,14 -333,9 +346,14 @@@ public class ColourSchemePropert
        ret = "T-Coffee Scores";
  
        break;
 +      
 +    case RNAINTERACTION:
 +        ret = "RNA Interaction type";
 +
 +        break;
      /*
       * case COVARIATION: ret = "Covariation";
-      *
+      * 
       * break;
       */
      case USER_DEFINED:
@@@ -497,16 -484,10 +502,16 @@@
  
      case TCOFFEE:
        cs = new TCoffeeColourScheme(coll);
 -      // case COVARIATION:
 -      // cs = new CovariationColourScheme(annotation);
 +      break;
 +      
 +    case RNAINTERACTION:
 +        cs = new RNAInteractionColourScheme();
 +        break;
 +      
 +    // case COVARIATION:
 +    // cs = new CovariationColourScheme(annotation);
  
-     // break;
+       // break;
  
      case USER_DEFINED:
        Color[] col = new Color[24];