From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 14 Oct 2013 16:26:20 +0000 (+0100)
Subject: Merge branch 'develop' into dev_from_2_8_1
X-Git-Tag: Jalview_2_9~221^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a9315b41e948f66f4632f7d419fda643bc0b9354;p=jalview.git

Merge branch 'develop' into dev_from_2_8_1

Conflicts:
	.classpath
	.project
	src/jalview/appletgui/AlignFrame.java
	src/jalview/io/FileLoader.java
---

a9315b41e948f66f4632f7d419fda643bc0b9354
diff --cc .classpath
index c22cae5,3ec9da3..22c4fce
--- a/.classpath
+++ b/.classpath
@@@ -39,14 -39,13 +39,14 @@@
  	<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
  	<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
  	<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
- 	<classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
 -	<classpathentry kind="lib" path="lib/min-jaba-client-2.0.jar" sourcepath="/clustengine2"/>
+ 	<classpathentry kind="lib" path="lib/Jmol-12.2.4.jar" sourcepath="/Users/jimp/Documents/e6-workspace-new/Jmol/src"/>
  	<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
  	<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
  	<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
  	<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
- 	<classpathentry kind="lib" path="lib/VARNAv3-9-dev.jar"/>
 +	<classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
 +	<classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
+ 	<classpathentry kind="lib" path="lib/VARNAv3-9.jar" sourcepath="/Users/jimp/Documents/Jalview/VARNA/VARNAv3-9-src.jar"/>
  	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
  	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
  	<classpathentry kind="output" path="classes"/>
diff --cc src/jalview/appletgui/AlignFrame.java
index 564f28c,4d574d6..8587cba
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@@ -1,3764 -1,3767 +1,3774 @@@
 -/*
 - * 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.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.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 == 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 == 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
 +/*
 + * 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.AlignViewControllerI;
 +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.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 jalview.util.MessageManager;
 +
 +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 AlignViewControllerI avc;
 +  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);
 +    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
 +    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(MessageManager.getString("label.successfully_added_features_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(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(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_G:
 +      if (evt.isControlDown())
 +      {
 +        if (evt.isShiftDown())
 +        {
 +          this.unGroup_actionPerformed();
 +        }
 +        else
 +        {
 +          this.createGroup_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, MessageManager.formatMessage("label.alignment_properties", new String[]{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 == RNAInteractionColour)
+     {
 -      viewport.applet.showURL(url, target);
++      changeColour(new RNAInteractionColourScheme());
+     }
 -  }
 -
 -  // ////////////////////////////////////////////////////////////////////////////////
 -  // 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();
 -
 +    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, MessageManager.getString("label.input_cut_paste"), 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,
 +    		MessageManager.formatMessage("label.alignment_output_command", new String[]{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(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
 +    cap.setAnnotationImport();
 +    Frame frame = new Frame();
 +    frame.add(cap);
 +    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.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, MessageManager.getString("label.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, MessageManager.getString("label.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(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
 +    }
 +    else
 +    {
 +      undoMenuItem.setEnabled(false);
 +      undoMenuItem.setLabel(MessageManager.getString("action.undo"));
 +    }
 +
 +    if (viewport.redoList.size() > 0)
 +    {
 +      redoMenuItem.setEnabled(true);
 +
 +      CommandI command = (CommandI) viewport.redoList.peek();
 +      redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
 +    }
 +    else
 +    {
 +      redoMenuItem.setEnabled(false);
 +      redoMenuItem.setLabel(MessageManager.getString("action.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 (avc.makeGroupsFromSelection()) {
 +      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
 +      alignPanel.updateAnnotation();
 +      alignPanel.paintAlignment(true);
 +    }
 +  }
 +
 +  protected void createGroup_actionPerformed()
 +  {
 +    avc.createGroup();
 +  }
 +  protected void unGroup_actionPerformed()
 +  {
 +    if (avc.unGroup())
 +    {
 +      alignPanel.alignmentChanged();
 +    }
 +  }
 +  protected void deleteGroups_actionPerformed()
 +  {
 +    if (avc.deleteGroups())
 +    {
 +      alignPanel.alignmentChanged();
 +    }
 +  }
 +
 +  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(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
 +      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(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
 +
 +    // 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, MessageManager.formatMessage("label.overview_params", new String[]{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, MessageManager.getString("action.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(MessageManager.getString("label.paste_newick_tree_file"));
 +    cap.setTreeImport();
 +    Frame frame = new Frame();
 +    frame.add(cap);
 +    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
 +  }
 +
 +  public void loadTree(jalview.io.NewickFile tree, String treeFile)
 +  {
 +    TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_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(MessageManager.formatMessage("label.order_by_params", new String[]{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(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
 +        g.setFont(new Font("Helvetica", Font.BOLD, 12));
 +        g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
 +        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
 +        g.drawString(
 +                MessageManager.getString("label.jalview_authors_1"),
 +                x, y += fh * 1.5);
 +        g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
 +        g.drawString(
 +                MessageManager.getString("label.jalview_dev_managers"),
 +                x, y += fh);
 +        g.drawString(
 +                MessageManager.getString("label.jalview_distribution_lists"),
 +                x, y += fh);
 +        g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
 +        g.drawString(
 +                MessageManager.getString("label.jalview_cite_1_authors"),
 +                x, y += fh);
 +        g.drawString(
 +                MessageManager.getString("label.jalview_cite_1_title"),
 +                x, y += fh);
 +        g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
 +                x, y += fh);
 +      }
 +    }
 +
 +    Frame frame = new Frame();
 +    frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
 +            .getBuildDate()));
 +    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.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(MessageManager.getString("action.file"));
 +
 +  MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
 +
 +  MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
 +
 +  MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
 +
 +  MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
 +
 +  MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
 +
 +  MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
 +
 +  Menu editMenu = new Menu(MessageManager.getString("action.edit"));
 +
 +  Menu viewMenu = new Menu(MessageManager.getString("action.view"));
 +
 +  Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
 +
 +  Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
 +
 +  MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
 +
 +  MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
 +
 +  MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.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();
 -
 -  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");
 +  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(MessageManager.getString("label.alignment_props"));
 +
 +  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 createGroup = new MenuItem();
 +
 +  MenuItem unGroup = 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(MessageManager.getString("action.remove_left"));
 +    remove2LeftMenuItem.addActionListener(this);
 +    remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
 +    remove2RightMenuItem.addActionListener(this);
 +    removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
 +    removeGappedColumnMenuItem.addActionListener(this);
 +    removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
 +    removeAllGapsMenuItem.addActionListener(this);
 +    viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
 +    viewBoxesMenuItem.setState(true);
 +    viewBoxesMenuItem.addItemListener(this);
 +    viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
 +    viewTextMenuItem.setState(true);
 +    viewTextMenuItem.addItemListener(this);
 +    sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
 +    sortPairwiseMenuItem.addActionListener(this);
 +    sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
 +    sortIDMenuItem.addActionListener(this);
 +    sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
 +    sortLengthMenuItem.addActionListener(this);
 +    sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
 +    sortGroupMenuItem.addActionListener(this);
 +    removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
 +    removeRedundancyMenuItem.addActionListener(this);
 +    pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
 +    pairwiseAlignmentMenuItem.addActionListener(this);
 +    PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
 +    PCAMenuItem.addActionListener(this);
 +    averageDistanceTreeMenuItem
 +            .setLabel(MessageManager.getString("label.average_distance_identity"));
 +    averageDistanceTreeMenuItem.addActionListener(this);
 +    neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
 +    neighbourTreeMenuItem.addActionListener(this);
 +    statusBar.setBackground(Color.white);
 +    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 +    statusBar.setText(MessageManager.getString("label.status_bar"));
 +    outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
 +    clustalColour.setLabel(MessageManager.getString("label.clustalx"));
 +
 +    clustalColour.addActionListener(this);
 +    zappoColour.setLabel(MessageManager.getString("label.zappo"));
 +    zappoColour.addActionListener(this);
 +    taylorColour.setLabel(MessageManager.getString("label.taylor"));
 +    taylorColour.addActionListener(this);
 +    hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
 +    hydrophobicityColour.addActionListener(this);
 +    helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
 +    helixColour.addActionListener(this);
 +    strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
 +    strandColour.addActionListener(this);
 +    turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
 +    turnColour.addActionListener(this);
 +    buriedColour.setLabel(MessageManager.getString("label.buried_index"));
 +    buriedColour.addActionListener(this);
 +    purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
 +    purinePyrimidineColour.addActionListener(this);
++    RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction"));
+     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.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);
 -    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);
 +    RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
 +    RNAHelixColour.addActionListener(this);
 +    userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
 +    userDefinedColour.addActionListener(this);
 +    PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
 +    PIDColour.addActionListener(this);
 +    BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
 +    BLOSUM62Colour.addActionListener(this);
 +    tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
 +    tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
 +                                     // provided
 +    tcoffeeColour.addActionListener(this);
 +    avDistanceTreeBlosumMenuItem
 +            .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
 +    avDistanceTreeBlosumMenuItem.addActionListener(this);
 +    njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
 +    njTreeBlosumMenuItem.addActionListener(this);
 +    annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
 +    annotationPanelMenuItem.addItemListener(this);
 +    colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
 +    colourTextMenuItem.addItemListener(this);
 +    displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
 +    displayNonconservedMenuItem.addItemListener(this);
 +    alProperties.addActionListener(this);
 +    overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
 +    overviewMenuItem.addActionListener(this);
 +    undoMenuItem.setEnabled(false);
 +    undoMenuItem.setLabel(MessageManager.getString("action.undo"));
 +    undoMenuItem.addActionListener(this);
 +    redoMenuItem.setEnabled(false);
 +    redoMenuItem.setLabel(MessageManager.getString("action.redo"));
 +    redoMenuItem.addActionListener(this);
 +    conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
 +    conservationMenuItem.addItemListener(this);
 +    noColourmenuItem.setLabel(MessageManager.getString("label.none"));
 +    noColourmenuItem.addActionListener(this);
 +    wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
 +    wrapMenuItem.addItemListener(this);
 +    renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
 +    renderGapsMenuItem.setState(true);
 +    renderGapsMenuItem.addItemListener(this);
 +    findMenuItem.setLabel(MessageManager.getString("action.find"));
 +    findMenuItem.addActionListener(this);
 +    abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
 +    abovePIDThreshold.addItemListener(this);
 +    nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
 +    nucleotideColour.addActionListener(this);
 +    deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
 +    deleteGroups.addActionListener(this);
 +    grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
 +    grpsFromSelection.addActionListener(this);
 +    createGroup.setLabel(MessageManager.getString("action.create_group"));
 +    unGroup.setLabel(MessageManager.getString("action.remove_group"));
 +    copy.setLabel(MessageManager.getString("action.copy"));
 +    copy.addActionListener(this);
 +    cut.setLabel(MessageManager.getString("action.cut"));
 +    cut.addActionListener(this);
 +    delete.setLabel(MessageManager.getString("action.delete"));
 +    delete.addActionListener(this);
 +    pasteMenu.setLabel(MessageManager.getString("action.paste"));
 +    pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
 +    pasteNew.addActionListener(this);
 +    pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
 +    pasteThis.addActionListener(this);
 +    applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
 +    applyToAllGroups.setState(true);
 +    applyToAllGroups.addItemListener(this);
 +    font.setLabel(MessageManager.getString("action.font"));
 +    font.addActionListener(this);
 +    scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
 +    scaleAbove.setState(true);
 +    scaleAbove.setEnabled(false);
 +    scaleAbove.addItemListener(this);
 +    scaleLeft.setEnabled(false);
 +    scaleLeft.setState(true);
 +    scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
 +    scaleLeft.addItemListener(this);
 +    scaleRight.setEnabled(false);
 +    scaleRight.setState(true);
 +    scaleRight.setLabel(MessageManager.getString("action.scale_right"));
 +    scaleRight.addItemListener(this);
 +    modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
 +    modifyPID.addActionListener(this);
 +    modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
 +    modifyConservation.addActionListener(this);
 +    sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
 +    sort.setLabel(MessageManager.getString("action.sort"));
 +    calculate.setLabel(MessageManager.getString("action.calculate_tree"));
 +    autoCalculate.addItemListener(this);
 +    sortByTree.addItemListener(this);
 +    inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
 +    inputText.addActionListener(this);
 +    centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
 +    centreColumnLabelFlag.addItemListener(this);
 +    followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
 +    followMouseOverFlag.addItemListener(this);
 +    helpMenu.setLabel(MessageManager.getString("action.help"));
 +    documentation.setLabel(MessageManager.getString("label.documentation"));
 +    documentation.addActionListener(this);
 +
 +    about.setLabel(MessageManager.getString("label.about"));
 +    about.addActionListener(this);
 +    seqLimits.setState(true);
 +    seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
 +    seqLimits.addItemListener(this);
 +    featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
 +    featureSettings.addActionListener(this);
 +    sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
 +    sequenceFeatures.addItemListener(this);
 +    sequenceFeatures.setState(false);
 +    annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
 +    annotationColour.addActionListener(this);
 +    invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
 +    invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
 +    menu1.setLabel(MessageManager.getString("action.show"));
 +    showColumns.setLabel(MessageManager.getString("label.all_columns"));
 +    showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
 +    menu2.setLabel(MessageManager.getString("aciton.hide"));
 +    hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
 +    hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
 +    hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
 +    hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
 +    showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
 +    showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
 +    showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
 +    showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
 +    showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
 +    normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
 +    applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
 +    applyAutoAnnotationSettings.setState(true);
 +    autoAnnMenu.setLabel(MessageManager.getString("label.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(MessageManager.getString("action.format"));
 +    selectMenu.setLabel(MessageManager.getString("action.select"));
 +    newView.setLabel(MessageManager.getString("action.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;
 -          }
 -        }
 -
 -        @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;
 -  }
 -
 -}
 +    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(createGroup);
 +    selectMenu.add(unGroup);
 +    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;
 +  }
 +
 +}
diff --cc src/jalview/io/FileLoader.java
index a8c60fd,ab5de61..2d59f29
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@@ -17,13 -17,18 +17,18 @@@
   */
  package jalview.io;
  
- import java.util.*;
 -import jalview.datamodel.Alignment;
+ import jalview.datamodel.AlignmentI;
+ import jalview.gui.AlignFrame;
+ import jalview.gui.AlignViewport;
+ import jalview.gui.Desktop;
+ import jalview.gui.Jalview2XML;
  
- import javax.swing.*;
+ import java.util.StringTokenizer;
+ import java.util.Vector;
  
- import jalview.datamodel.*;
- import jalview.gui.*;
 +import jalview.util.MessageManager;
+ import javax.swing.JOptionPane;
+ import javax.swing.SwingUtilities;
  
  public class FileLoader implements Runnable
  {