X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=ce710349ab969d6b2fa73c7e7d3ee1c04072bc4d;hb=a581135c768ce6c60c38bbd47003477f8c557eea;hp=1377de2b1fef0fab631c3e63a3efced38ca90076;hpb=3dc211ddfada6bd9036697ec8236c188f131b84f;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1377de2..ce71034 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,934 +1,1556 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import MCview.*;
-
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class PopupMenu extends JPopupMenu
-{
-    JMenu groupMenu = new JMenu();
-    JMenuItem groupName = new JMenuItem();
-    protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-    protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
-    protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-    JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-    protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-    AlignmentPanel ap;
-    JMenu sequenceMenu = new JMenu();
-    JMenuItem sequenceName = new JMenuItem();
-    Sequence sequence;
-    JMenuItem unGroupMenuItem = new JMenuItem();
-    JMenuItem pdbMenuItem = new JMenuItem();
-    JMenuItem outline = new JMenuItem();
-    JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
-    JMenu colourMenu = new JMenu();
-    JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
-    JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
-    JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-
-    /**
-     * Creates a new PopupMenu object.
-     *
-     * @param ap DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     */
-    public PopupMenu(AlignmentPanel ap, Sequence seq)
-    {
-        ///////////////////////////////////////////////////////////
-        // If this is activated from the sequence panel, the user may want to
-        // edit or annotate a particular residue. Therefore display the residue menu
-        //
-        // If from the IDPanel, we must display the sequence menu
-        //////////////////////////////////////////////////////////
-        this.ap = ap;
-        sequence = seq;
-
-        ButtonGroup colours = new ButtonGroup();
-        colours.add(noColourmenuItem);
-        colours.add(clustalColour);
-        colours.add(zappoColour);
-        colours.add(taylorColour);
-        colours.add(hydrophobicityColour);
-        colours.add(helixColour);
-        colours.add(strandColour);
-        colours.add(turnColour);
-        colours.add(buriedColour);
-        colours.add(abovePIDColour);
-        colours.add(userDefinedColour);
-        colours.add(PIDColour);
-        colours.add(BLOSUM62Colour);
-
-        try
-        {
-            jbInit();
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
-
-        if ((seq == null) || (seq.getPDBId() == null))
-        {
-            pdbMenuItem.setVisible(false);
-        }
-
-        SequenceGroup sg = ap.av.getSelectionGroup();
-
-        if (sg != null)
-        {
-            groupName.setText(sg.getName());
-
-            if (sg.cs instanceof ZappoColourScheme)
-            {
-                zappoColour.setSelected(true);
-            }
-            else if (sg.cs instanceof TaylorColourScheme)
-            {
-                taylorColour.setSelected(true);
-            }
-            else if (sg.cs instanceof PIDColourScheme)
-            {
-                PIDColour.setSelected(true);
-            }
-            else if (sg.cs instanceof Blosum62ColourScheme)
-            {
-                BLOSUM62Colour.setSelected(true);
-            }
-            else if (sg.cs instanceof UserColourScheme)
-            {
-                userDefinedColour.setSelected(true);
-            }
-            else if (sg.cs instanceof HydrophobicColourScheme)
-            {
-                hydrophobicityColour.setSelected(true);
-            }
-            else if (sg.cs instanceof HelixColourScheme)
-            {
-                helixColour.setSelected(true);
-            }
-            else if (sg.cs instanceof StrandColourScheme)
-            {
-                strandColour.setSelected(true);
-            }
-            else if (sg.cs instanceof TurnColourScheme)
-            {
-                turnColour.setSelected(true);
-            }
-            else if (sg.cs instanceof BuriedColourScheme)
-            {
-                buriedColour.setSelected(true);
-            }
-            else if (sg.cs instanceof ClustalxColourScheme)
-            {
-                clustalColour.setSelected(true);
-            }
-            else
-            {
-                noColourmenuItem.setSelected(true);
-            }
-
-            if (sg.cs!=null && sg.cs.conservationApplied())
-            {
-                conservationMenuItem.setSelected(true);
-            }
-
-            showText.setSelected(sg.getDisplayText());
-            showColourText.setSelected(sg.getColourText());
-            showBoxes.setSelected(sg.getDisplayBoxes());
-        }
-
-        if (!ap.av.alignment.getGroups().contains(sg))
-        {
-            unGroupMenuItem.setVisible(false);
-        }
-        else
-        {
-            groupMenu.insertSeparator(3);
-        }
-
-        if (seq == null)
-        {
-            sequenceMenu.setVisible(false);
-        }
-        else
-        {
-          java.util.Vector links = Preferences.sequenceURLLinks;
-
-          JMenu linkMenu = new JMenu("Link");
-          JMenuItem item;
-          for(int i=0; i<links.size(); i++)
-          {
-            String link = links.elementAt(i).toString();
-
-            item = new JMenuItem(link.substring(0, link.indexOf("|")));
-
-            final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-                + sequence.getName() +
-                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
-
-
-            item.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    showLink(url);
-                }
-            });
-
-            linkMenu.add(item);
-          }
-          add(linkMenu);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
-    {
-        groupMenu.setText("Group");
-        groupMenu.setText("Define");
-        groupName.setText("Name");
-        groupName.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    groupName_actionPerformed(e);
-                }
-            });
-        sequenceMenu.setText("Sequence");
-        sequenceName.setText("Edit name");
-        sequenceName.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    sequenceName_actionPerformed(e);
-                }
-            });
-        PIDColour.setFocusPainted(false);
-        unGroupMenuItem.setText("Remove Group");
-        unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    unGroupMenuItem_actionPerformed(e);
-                }
-            });
-        pdbMenuItem.setText("View PDB structure");
-        pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    pdbMenuItem_actionPerformed(e);
-                }
-            });
-        outline.setText("Border colour");
-        outline.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    outline_actionPerformed(e);
-                }
-            });
-        nucleotideMenuItem.setText("Nucleotide");
-        nucleotideMenuItem.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    nucleotideMenuItem_actionPerformed(e);
-                }
-            });
-        colourMenu.setText("Group Colour");
-        showBoxes.setText("Boxes");
-        showBoxes.setState(true);
-        showBoxes.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    showBoxes_actionPerformed(e);
-                }
-            });
-        showText.setText("Text");
-        showText.setState(true);
-        showText.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    showText_actionPerformed(e);
-                }
-            });
-        showColourText.setText("Colour Text");
-        showColourText.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    showColourText_actionPerformed(e);
-                }
-            });
-        add(groupMenu);
-        add(sequenceMenu);
-        groupMenu.add(groupName);
-        groupMenu.addSeparator();
-        groupMenu.add(unGroupMenuItem);
-        groupMenu.add(colourMenu);
-        groupMenu.addSeparator();
-        groupMenu.add(showBoxes);
-        groupMenu.add(showText);
-        groupMenu.add(showColourText);
-        groupMenu.addSeparator();
-        groupMenu.add(outline);
-        sequenceMenu.add(sequenceName);
-        sequenceMenu.add(pdbMenuItem);
-        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(nucleotideMenuItem);
-        colourMenu.add(userDefinedColour);
-
-        if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
-        {
-          java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-              getUserColourSchemes().keys();
-
-          while (userColours.hasMoreElements())
-          {
-            JMenuItem item = new JMenuItem(userColours.
-                nextElement().toString());
-            item.addActionListener(new ActionListener()
-            {
-              public void actionPerformed(ActionEvent evt)
-              {
-                userDefinedColour_actionPerformed(evt);
-              }
-            });
-            colourMenu.add(item);
-          }
-        }
-
-
-        colourMenu.addSeparator();
-        colourMenu.add(abovePIDColour);
-        colourMenu.add(conservationMenuItem);
-        noColourmenuItem.setText("None");
-        noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    noColourmenuItem_actionPerformed(e);
-                }
-            });
-
-        clustalColour.setText("Clustalx colours");
-        clustalColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    clustalColour_actionPerformed(e);
-                }
-            });
-        zappoColour.setText("Zappo");
-        zappoColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    zappoColour_actionPerformed(e);
-                }
-            });
-        taylorColour.setText("Taylor");
-        taylorColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    taylorColour_actionPerformed(e);
-                }
-            });
-        hydrophobicityColour.setText("Hydrophobicity");
-        hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    hydrophobicityColour_actionPerformed(e);
-                }
-            });
-        helixColour.setText("Helix propensity");
-        helixColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    helixColour_actionPerformed(e);
-                }
-            });
-        strandColour.setText("Strand propensity");
-        strandColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    strandColour_actionPerformed(e);
-                }
-            });
-        turnColour.setText("Turn propensity");
-        turnColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    turnColour_actionPerformed(e);
-                }
-            });
-        buriedColour.setText("Buried Index");
-        buriedColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    buriedColour_actionPerformed(e);
-                }
-            });
-        abovePIDColour.setText("Above % Identity");
-        abovePIDColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    abovePIDColour_actionPerformed(e);
-                }
-            });
-        userDefinedColour.setText("User Defined...");
-        userDefinedColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    userDefinedColour_actionPerformed(e);
-                }
-            });
-        PIDColour.setText("Percentage Identity");
-        PIDColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    PIDColour_actionPerformed(e);
-                }
-            });
-        BLOSUM62Colour.setText("BLOSUM62");
-        BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    BLOSUM62Colour_actionPerformed(e);
-                }
-            });
-        conservationMenuItem.setText("Conservation");
-        conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    conservationMenuItem_actionPerformed(e);
-                }
-            });
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    void refresh()
-    {
-        SequenceGroup sg = getGroup();
-        if(sg!=null)
-        {
-          SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
-          if (superG != null)
-          {
-            superG.setSuperGroupProperties(sg);
-          }
-        }
-        if (ap.overviewPanel != null)
-          ap.overviewPanel.updateOverviewImage();
-
-        ap.seqPanel.repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void clustalColour_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = getGroup();
-        sg.cs = new ClustalxColourScheme(sg.sequences,
-                ap.av.alignment.getWidth());
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void zappoColour_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = new ZappoColourScheme();
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void taylorColour_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = new TaylorColourScheme();
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = new HydrophobicColourScheme();
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void helixColour_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = new HelixColourScheme();
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void strandColour_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = new StrandColourScheme();
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void turnColour_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = new TurnColourScheme();
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void buriedColour_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = new BuriedColourScheme();
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void nucleotideMenuItem_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = new NucleotideColourScheme();
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void abovePIDColour_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = getGroup();
-        if(sg.cs==null)
-          return;
-
-        if (abovePIDColour.isSelected())
-        {
-            sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                    ap.av.alignment.getWidth()));
-
-            int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
-                    getGroup().getName());
-
-           sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
-
-            SliderPanel.showPIDSlider();
-        }
-        else // remove PIDColouring
-        {
-            sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
-        }
-
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void userDefinedColour_actionPerformed(ActionEvent e)
-    {
-       SequenceGroup sg = getGroup();
-
-       if (e.getActionCommand().equals("User Defined..."))
-         new UserDefinedColours(ap, sg);
-       else
-       {
-         UserColourScheme udc = (UserColourScheme) UserDefinedColours.
-             getUserColourSchemes().get(e.getActionCommand());
-
-         sg.cs = udc;
-       }
-     }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void PIDColour_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = getGroup();
-        sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                ap.av.alignment.getWidth()));
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = getGroup();
-
-        sg.cs = new Blosum62ColourScheme();
-
-        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                ap.av.alignment.getWidth()));
-
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void noColourmenuItem_actionPerformed(ActionEvent e)
-    {
-        getGroup().cs = null;
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void conservationMenuItem_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = getGroup();
-        if(sg.cs==null)
-          return;
-
-        if (conservationMenuItem.isSelected())
-        {
-            Conservation c = new Conservation("Group",
-                    ResidueProperties.propHash, 3, sg.sequences, 0,
-                    ap.av.alignment.getWidth());
-
-            c.calculate();
-            c.verdict(false, ap.av.ConsPercGaps);
-
-            sg.cs.setConservation(c);
-
-            SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
-            SliderPanel.showConservationSlider();
-        }
-        else // remove ConservationColouring
-        {
-            sg.cs.setConservation(null);
-        }
-
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void groupName_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = getGroup();
-        String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                "Enter new group name", "Edit group name",
-                JOptionPane.QUESTION_MESSAGE);
-
-        if (reply == null)
-        {
-            return;
-        }
-
-        sg.setName(reply);
-        groupName.setText(reply);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void analyze_actionPerformed(ActionEvent e)
-    {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        JInternalFrame frame = new JInternalFrame();
-        frame.setContentPane(cap);
-        Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
-
-        SequenceGroup sg = getGroup();
-        StringBuffer sb = new StringBuffer();
-
-        for (int i = 0; i < sg.sequences.size(); i++)
-        {
-            Sequence tmp = (Sequence) sg.sequences.get(i);
-            sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
-            sb.append("\n");
-        }
-
-        sb.append("Something amazing will happen soon");
-        cap.setText(sb.toString());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    SequenceGroup getGroup()
-    {
-        SequenceGroup sg = ap.av.getSelectionGroup();
-      // this method won't add a new group if it already exists
-        if(sg!=null)
-          ap.av.alignment.addGroup(sg);
-
-        return sg;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    void sequenceName_actionPerformed(ActionEvent e)
-    {
-        String id = sequence.getName();
-        String s = (String) JOptionPane.showInternalInputDialog(ap,
-                "Edit sequence name",
-                "Edit sequence name (" + sequence.getName() + ")",
-                JOptionPane.PLAIN_MESSAGE, null, null, id);
-
-        if (s != null)
-        {
-            if (s.indexOf(" ") > -1)
-            {
-                JOptionPane.showMessageDialog(ap,
-                    "Spaces have been converted to \"_\"",
-                    "No spaces allowed in Sequence Name",
-                    JOptionPane.WARNING_MESSAGE);
-            }
-
-            s = s.replace(' ', '_');
-            sequence.setName(s);
-            ap.repaint();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    void unGroupMenuItem_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = ap.av.getSelectionGroup();
-        ap.av.alignment.deleteGroup(sg);
-        ap.av.setSelectionGroup(null);
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    void pdbMenuItem_actionPerformed(ActionEvent e)
-    {
-        if (sequence.getPDBId() == null)
-        {
-            return;
-        }
-
-        try
-        {
-            EBIFetchClient ebi = new EBIFetchClient();
-            String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
-                    null);
-
-            PDBfile pdb = new PDBfile(result);
-
-            rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
-            JInternalFrame frame = new JInternalFrame();
-            frame.setContentPane(rc);
-            Desktop.addInternalFrame(frame,
-                sequence.getName() + " " + sequence.getPDBId(), 400, 400);
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void outline_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = getGroup();
-        Color col = JColorChooser.showDialog(this, "Select Outline Colour",
-                Color.BLUE);
-
-        if (col != null)
-        {
-            sg.setOutlineColour(col);
-        }
-
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void showBoxes_actionPerformed(ActionEvent e)
-    {
-        getGroup().setDisplayBoxes(showBoxes.isSelected());
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void showText_actionPerformed(ActionEvent e)
-    {
-        getGroup().setDisplayText(showText.isSelected());
-        refresh();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void showColourText_actionPerformed(ActionEvent e)
-    {
-        getGroup().setColourText(showColourText.isSelected());
-        refresh();
-    }
-
-    public void showLink(String url)
-    {
-      try
-      {
-        jalview.util.BrowserLauncher.openURL(url);
-      }
-      catch (Exception ex)
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            "Unixers: Couldn't find default web browser."
-           +"\nAdd the full path to your browser in Preferences.",
-           "Web browser not found", JOptionPane.WARNING_MESSAGE );
-
-
-        ex.printStackTrace();
-      }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import MCview.*;
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.util.UrlLink;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PopupMenu
+    extends JPopupMenu
+{
+  JMenu groupMenu = new JMenu();
+  JMenuItem groupName = new JMenuItem();
+  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem hydrophobicityColour = new
+      JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+  protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  AlignmentPanel ap;
+  JMenu sequenceMenu = new JMenu();
+  JMenuItem sequenceName = new JMenuItem();
+  Sequence sequence;
+  JMenuItem unGroupMenuItem = new JMenuItem();
+  JMenuItem outline = new JMenuItem();
+  JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+  JMenu colourMenu = new JMenu();
+  JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+  JMenu editMenu = new JMenu();
+  JMenuItem cut = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem upperCase = new JMenuItem();
+  JMenuItem lowerCase = new JMenuItem();
+  JMenuItem toggle = new JMenuItem();
+  JMenu pdbMenu = new JMenu();
+  JMenuItem pdbFromFile = new JMenuItem();
+  JMenuItem enterPDB = new JMenuItem();
+  JMenuItem discoverPDB = new JMenuItem();
+  JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+  JMenu structureMenu = new JMenu();
+  JMenu viewStructureMenu = new JMenu();
+ // JMenu colStructureMenu = new JMenu();
+  JMenuItem editSequence = new JMenuItem();
+ // JMenuItem annotationMenuItem = new JMenuItem();
+
+  /**
+   * Creates a new PopupMenu object.
+   *
+   * @param ap DOCUMENT ME!
+   * @param seq DOCUMENT ME!
+   */
+  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+  {
+    ///////////////////////////////////////////////////////////
+    // If this is activated from the sequence panel, the user may want to
+    // edit or annotate a particular residue. Therefore display the residue menu
+    //
+    // If from the IDPanel, we must display the sequence menu
+    //////////////////////////////////////////////////////////
+    this.ap = ap;
+    sequence = seq;
+
+    ButtonGroup colours = new ButtonGroup();
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(abovePIDColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+
+    for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+    {
+      JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
+                                     i]);
+
+      item.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          outputText_actionPerformed(e);
+        }
+      });
+
+      outputMenu.add(item);
+    }
+
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if (seq != null)
+    {
+      sequenceMenu.setText(sequence.getName());
+
+      JMenuItem menuItem;
+      if (seq.getDatasetSequence().getPDBId() != null
+          && seq.getDatasetSequence().getPDBId().size()>0)
+      {
+        java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+            elements();
+
+        while (e.hasMoreElements())
+        {
+          final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+          menuItem = new JMenuItem();
+          menuItem.setText(pdb.getId());
+          menuItem.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              Vector seqs = new Vector();
+              for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+              {
+                Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
+                if(pdbs==null)
+                  continue;
+
+                for(int p=0; p<pdbs.size(); p++)
+                {
+                  PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
+                  if(p1.getId().equals(pdb.getId()))
+                  {
+                    if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
+                        seqs.addElement(ap.av.alignment.getSequenceAt(i));
+
+                      continue;
+                  }
+                }
+              }
+
+              SequenceI [] seqs2 = new SequenceI[seqs.size()];
+              seqs.toArray(seqs2);
+
+              new AppJmol(pdb, seqs2, null, ap);
+              //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+            }
+          });
+          viewStructureMenu.add(menuItem);
+
+       /*   menuItem = new JMenuItem();
+          menuItem.setText(pdb.getId());
+          menuItem.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              colourByStructure(pdb.getId());
+            }
+          });
+          colStructureMenu.add(menuItem);*/
+        }
+      }
+      else
+      {
+        structureMenu.remove(viewStructureMenu);
+       // structureMenu.remove(colStructureMenu);
+      }
+
+      menuItem = new JMenuItem("Hide Sequences");
+      menuItem.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          hideSequences(false);
+        }
+      });
+      add(menuItem);
+
+      if (ap.av.getSelectionGroup() != null
+          && ap.av.getSelectionGroup().getSize() > 1)
+      {
+        menuItem = new JMenuItem("Represent Group with " + seq.getName());
+        menuItem.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            hideSequences(true);
+          }
+        });
+        sequenceMenu.add(menuItem);
+      }
+
+      if (ap.av.hasHiddenRows)
+      {
+        final int index = ap.av.alignment.findIndex(seq);
+
+        if (ap.av.adjustForHiddenSeqs(index) -
+            ap.av.adjustForHiddenSeqs(index - 1) > 1)
+        {
+          menuItem = new JMenuItem("Reveal Sequences");
+          menuItem.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              ap.av.showSequence(index);
+              if (ap.overviewPanel != null)
+              {
+                ap.overviewPanel.updateOverviewImage();
+              }
+            }
+          });
+          add(menuItem);
+        }
+
+        menuItem = new JMenuItem("Reveal All");
+        menuItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            ap.av.showAllHiddenSeqs();
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+
+        add(menuItem);
+      }
+
+    }
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      groupName.setText(sg.getName());
+
+      if (sg.cs instanceof ZappoColourScheme)
+      {
+        zappoColour.setSelected(true);
+      }
+      else if (sg.cs instanceof TaylorColourScheme)
+      {
+        taylorColour.setSelected(true);
+      }
+      else if (sg.cs instanceof PIDColourScheme)
+      {
+        PIDColour.setSelected(true);
+      }
+      else if (sg.cs instanceof Blosum62ColourScheme)
+      {
+        BLOSUM62Colour.setSelected(true);
+      }
+      else if (sg.cs instanceof UserColourScheme)
+      {
+        userDefinedColour.setSelected(true);
+      }
+      else if (sg.cs instanceof HydrophobicColourScheme)
+      {
+        hydrophobicityColour.setSelected(true);
+      }
+      else if (sg.cs instanceof HelixColourScheme)
+      {
+        helixColour.setSelected(true);
+      }
+      else if (sg.cs instanceof StrandColourScheme)
+      {
+        strandColour.setSelected(true);
+      }
+      else if (sg.cs instanceof TurnColourScheme)
+      {
+        turnColour.setSelected(true);
+      }
+      else if (sg.cs instanceof BuriedColourScheme)
+      {
+        buriedColour.setSelected(true);
+      }
+      else if (sg.cs instanceof ClustalxColourScheme)
+      {
+        clustalColour.setSelected(true);
+      }
+      else
+      {
+        noColourmenuItem.setSelected(true);
+      }
+
+      if (sg.cs != null && sg.cs.conservationApplied())
+      {
+        conservationMenuItem.setSelected(true);
+      }
+
+      showText.setSelected(sg.getDisplayText());
+      showColourText.setSelected(sg.getColourText());
+      showBoxes.setSelected(sg.getDisplayBoxes());
+    }
+    else
+    {
+      groupMenu.setVisible(false);
+      editMenu.setVisible(false);
+    }
+
+    if (!ap.av.alignment.getGroups().contains(sg))
+    {
+      unGroupMenuItem.setVisible(false);
+    }
+
+    if (seq == null)
+    {
+      sequenceMenu.setVisible(false);
+      structureMenu.setVisible(false);
+    }
+
+    if (links != null && links.size() > 0)
+    {
+      JMenu linkMenu = new JMenu("Link");
+
+      for (int i = 0; i < links.size(); i++)
+      {
+        String link = links.elementAt(i).toString();
+        UrlLink urlLink = null;
+        try {
+          urlLink = new UrlLink(link);
+        } catch (Exception foo) {
+          jalview.bin.Cache.log.error("Exception for URLLink '"+link+"'",foo);
+          continue;
+        };
+        if (!urlLink.isValid())
+        {
+          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+          continue;
+        }
+        final String label = urlLink.getLabel();
+        if (urlLink.isDynamic())
+        {
+
+          // collect matching db-refs
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{urlLink.getTarget()});
+          // collect id string too
+          String id = seq.getName();
+          if (dbr!=null)
+          {
+            for (int r=0;r<dbr.length; r++)
+            {
+              if (id!=null && dbr[r].getAccessionId().equals(id))
+              {
+                // suppress duplicate link creation for the bare sequence ID string with this link
+                id = null;
+              }
+              // create Bare ID link for this RUL
+              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
+              if (urls!=null)
+              {
+                for (int u=0; u<urls.length; u+=2)
+                {
+                  addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]); 
+                }
+              }
+            }
+          }
+          if (id!=null)
+          {
+            // create Bare ID link for this RUL
+            String[] urls = urlLink.makeUrls(id, true);
+            if (urls!=null)
+            {
+              for (int u=0; u<urls.length; u+=2)
+              {
+                addshowLink(linkMenu, label,  urls[u+1]);
+              }
+            }
+          }
+        } else
+        {
+          // Add a non-dynamic link
+          addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+        }
+      }
+      if (sequence != null)
+      {
+        sequenceMenu.add(linkMenu);
+      }
+      else
+      {
+        add(linkMenu);
+      }
+    }
+  }
+
+  /**
+   * add a show URL menu item to the given linkMenu
+   * @param linkMenu
+   * @param label - menu label string
+   * @param url - url to open
+   */
+  private void addshowLink(JMenu linkMenu, String label, final String url)
+  {
+    JMenuItem item = new JMenuItem(label);
+    item.setToolTipText("open URL: "+url);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        new Thread(new Runnable() {
+
+          public void run()
+          {
+            showLink(url);
+          }
+          
+        }).start();
+      }
+    });
+
+    linkMenu.add(item);    
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    groupMenu.setText("Group");
+    groupMenu.setText("Selection");
+    groupName.setText("Name");
+    groupName.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        groupName_actionPerformed();
+      }
+    });
+    sequenceMenu.setText("Sequence");
+    sequenceName.setText("Edit Name/Description");
+    sequenceName.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceName_actionPerformed();
+      }
+    });
+    PIDColour.setFocusPainted(false);
+    unGroupMenuItem.setText("Remove Group");
+    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        unGroupMenuItem_actionPerformed();
+      }
+    });
+
+    outline.setText("Border colour");
+    outline.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        outline_actionPerformed();
+      }
+    });
+    nucleotideMenuItem.setText("Nucleotide");
+    nucleotideMenuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideMenuItem_actionPerformed();
+      }
+    });
+    colourMenu.setText("Group Colour");
+    showBoxes.setText("Boxes");
+    showBoxes.setState(true);
+    showBoxes.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showBoxes_actionPerformed();
+      }
+    });
+    showText.setText("Text");
+    showText.setState(true);
+    showText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showText_actionPerformed();
+      }
+    });
+    showColourText.setText("Colour Text");
+    showColourText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showColourText_actionPerformed();
+      }
+    });
+    editMenu.setText("Edit");
+    cut.setText("Cut");
+    cut.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed();
+      }
+    });
+    upperCase.setText("To Upper Case");
+    upperCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    copy.setText("Copy");
+    copy.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed();
+      }
+    });
+    lowerCase.setText("To Lower Case");
+    lowerCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    toggle.setText("Toggle Case");
+    toggle.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    pdbMenu.setText("Associate Structure with Sequence");
+    pdbFromFile.setText("From File");
+    pdbFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pdbFromFile_actionPerformed();
+      }
+    });
+    enterPDB.setText("Enter PDB Id");
+    enterPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        enterPDB_actionPerformed();
+      }
+    });
+    discoverPDB.setText("Discover PDB ids");
+    discoverPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        discoverPDB_actionPerformed();
+      }
+    });
+    outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed();
+      }
+    });
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed();
+      }
+    });
+    jMenu1.setText("Group");
+    structureMenu.setText("Structure");
+    viewStructureMenu.setText("View Structure");
+  //  colStructureMenu.setText("Colour By Structure");
+    editSequence.setText("Edit Sequence...");
+    editSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        editSequence_actionPerformed(actionEvent);
+      }
+    });
+   /* annotationMenuItem.setText("By Annotation");
+    annotationMenuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        annotationMenuItem_actionPerformed(actionEvent);
+      }
+    });*/
+
+    add(groupMenu);
+
+    add(sequenceMenu);
+    this.add(structureMenu);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputMenu);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(jMenu1);
+    sequenceMenu.add(sequenceName);
+    colourMenu.add(textColour);
+    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(nucleotideMenuItem);
+    colourMenu.add(userDefinedColour);
+
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        JMenuItem item = new JMenuItem(userColours.
+                                       nextElement().toString());
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.add(item);
+      }
+    }
+
+    colourMenu.addSeparator();
+    colourMenu.add(abovePIDColour);
+    colourMenu.add(conservationMenuItem);
+    //colourMenu.add(annotationMenuItem);
+    editMenu.add(copy);
+    editMenu.add(cut);
+    editMenu.add(editSequence);
+    editMenu.add(upperCase);
+    editMenu.add(lowerCase);
+    editMenu.add(toggle);
+    pdbMenu.add(pdbFromFile);
+    pdbMenu.add(enterPDB);
+    pdbMenu.add(discoverPDB);
+    jMenu1.add(groupName);
+    jMenu1.add(unGroupMenuItem);
+    jMenu1.add(colourMenu);
+    jMenu1.add(showBoxes);
+    jMenu1.add(showText);
+    jMenu1.add(showColourText);
+    jMenu1.add(outline);
+    structureMenu.add(pdbMenu);
+    structureMenu.add(viewStructureMenu);
+   // structureMenu.add(colStructureMenu);
+    noColourmenuItem.setText("None");
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed();
+      }
+    });
+
+    clustalColour.setText("Clustalx colours");
+    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clustalColour_actionPerformed();
+      }
+    });
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zappoColour_actionPerformed();
+      }
+    });
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        taylorColour_actionPerformed();
+      }
+    });
+    hydrophobicityColour.setText("Hydrophobicity");
+    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hydrophobicityColour_actionPerformed();
+      }
+    });
+    helixColour.setText("Helix propensity");
+    helixColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        helixColour_actionPerformed();
+      }
+    });
+    strandColour.setText("Strand propensity");
+    strandColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        strandColour_actionPerformed();
+      }
+    });
+    turnColour.setText("Turn propensity");
+    turnColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        turnColour_actionPerformed();
+      }
+    });
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        buriedColour_actionPerformed();
+      }
+    });
+    abovePIDColour.setText("Above % Identity");
+    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDColour_actionPerformed();
+      }
+    });
+    userDefinedColour.setText("User Defined...");
+    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        userDefinedColour_actionPerformed(e);
+      }
+    });
+    PIDColour.setText("Percentage Identity");
+    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PIDColour_actionPerformed();
+      }
+    });
+    BLOSUM62Colour.setText("BLOSUM62");
+    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        BLOSUM62Colour_actionPerformed();
+      }
+    });
+    conservationMenuItem.setText("Conservation");
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed();
+      }
+    });
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  void refresh()
+  {
+    ap.paintAlignment(true);
+
+    PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void clustalColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
+                                     ap.av.alignment.getWidth());
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void zappoColour_actionPerformed()
+  {
+    getGroup().cs = new ZappoColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void taylorColour_actionPerformed()
+  {
+    getGroup().cs = new TaylorColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void hydrophobicityColour_actionPerformed()
+  {
+    getGroup().cs = new HydrophobicColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void helixColour_actionPerformed()
+  {
+    getGroup().cs = new HelixColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void strandColour_actionPerformed()
+  {
+    getGroup().cs = new StrandColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void turnColour_actionPerformed()
+  {
+    getGroup().cs = new TurnColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void buriedColour_actionPerformed()
+  {
+    getGroup().cs = new BuriedColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void nucleotideMenuItem_actionPerformed()
+  {
+    getGroup().cs = new NucleotideColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void abovePIDColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs == null)
+    {
+      return;
+    }
+
+    if (abovePIDColour.isSelected())
+    {
+      sg.cs.setConsensus(AAFrequency.calculate(
+          sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+          sg.getEndRes() + 1));
+
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
+
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+
+      SliderPanel.showPIDSlider();
+    }
+    else // remove PIDColouring
+    {
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+    }
+
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = getGroup();
+
+    if (e.getActionCommand().equals("User Defined..."))
+    {
+      new UserDefinedColours(ap, sg);
+    }
+    else
+    {
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+          getUserColourSchemes().get(e.getActionCommand());
+
+      sg.cs = udc;
+    }
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void PIDColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    sg.cs = new PIDColourScheme();
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences),
+                                             sg.getStartRes(),
+                                             sg.getEndRes() + 1));
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void BLOSUM62Colour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+
+    sg.cs = new Blosum62ColourScheme();
+
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences),
+                                             sg.getStartRes(),
+                                             sg.getEndRes() + 1));
+
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void noColourmenuItem_actionPerformed()
+  {
+    getGroup().cs = null;
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void conservationMenuItem_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs == null)
+    {
+      return;
+    }
+
+    if (conservationMenuItem.isSelected())
+    {
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3,
+                                        sg.getSequences(ap.av.
+          hiddenRepSequences),
+                                        sg.getStartRes(),
+                                        sg.getEndRes() + 1);
+
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
+
+      sg.cs.setConservation(c);
+
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+      SliderPanel.showConservationSlider();
+    }
+    else // remove ConservationColouring
+    {
+      sg.cs.setConservation(null);
+    }
+
+    refresh();
+  }
+
+  public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
+  {
+    SequenceGroup sg = getGroup();
+    if (sg == null)
+    {
+      return;
+    }
+
+    AnnotationColourGradient acg = new AnnotationColourGradient(
+        sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
+
+    acg.predefinedColours = true;
+    sg.cs = acg;
+
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void groupName_actionPerformed()
+  {
+
+    SequenceGroup sg = getGroup();
+    EditNameDialog dialog = new EditNameDialog(sg.getName(),
+                                               sg.getDescription(),
+                                               "       Group Name ",
+                                               "Group Description ",
+                                               "Edit Group Name/Description");
+
+    if (!dialog.accept)
+    {
+      return;
+    }
+
+    sg.setName(dialog.getName());
+    sg.setDescription(dialog.getDescription());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  SequenceGroup getGroup()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    // this method won't add a new group if it already exists
+    if (sg != null)
+    {
+      ap.av.alignment.addGroup(sg);
+    }
+
+    return sg;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  void sequenceName_actionPerformed()
+  {
+    EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+                                               sequence.getDescription(),
+                                               "       Sequence Name ",
+                                               "Sequence Description ",
+                                               "Edit Sequence Name/Description");
+
+    if (!dialog.accept)
+    {
+      return;
+    }
+
+    if (dialog.getName() != null)
+    {
+      if (dialog.getName().indexOf(" ") > -1)
+      {
+        JOptionPane.showMessageDialog(ap,
+                                      "Spaces have been converted to \"_\"",
+                                      "No spaces allowed in Sequence Name",
+                                      JOptionPane.WARNING_MESSAGE);
+      }
+
+      sequence.setName(dialog.getName().replace(' ', '_'));
+      ap.paintAlignment(false);
+    }
+
+    sequence.setDescription(dialog.getDescription());
+
+    ap.av.firePropertyChange("alignment", null,
+                             ap.av.getAlignment().getSequences());
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  void unGroupMenuItem_actionPerformed()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void outline_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+                                         Color.BLUE);
+
+    if (col != null)
+    {
+      sg.setOutlineColour(col);
+    }
+
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showBoxes_actionPerformed()
+  {
+    getGroup().setDisplayBoxes(showBoxes.isSelected());
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showText_actionPerformed()
+  {
+    getGroup().setDisplayText(showText.isSelected());
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showColourText_actionPerformed()
+  {
+    getGroup().setColourText(showColourText.isSelected());
+    refresh();
+  }
+
+  public void showLink(String url)
+  {
+    try
+    {
+      jalview.util.BrowserLauncher.openURL(url);
+    }
+    catch (Exception ex)
+    {
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "Unixers: Couldn't find default web browser."
+                                            +
+          "\nAdd the full path to your browser in Preferences.",
+                                            "Web browser not found",
+                                            JOptionPane.WARNING_MESSAGE);
+
+      ex.printStackTrace();
+    }
+  }
+
+  void hideSequences(boolean representGroup)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null || sg.getSize() < 1)
+    {
+      ap.av.hideSequence(new SequenceI[]
+                         {sequence});
+      return;
+    }
+
+    ap.av.setSelectionGroup(null);
+
+    if (representGroup)
+    {
+      ap.av.hideRepSequences(sequence, sg);
+
+      return;
+    }
+
+    int gsize = sg.getSize();
+    SequenceI[] hseqs;
+
+    hseqs = new SequenceI[gsize];
+
+    int index = 0;
+    for (int i = 0; i < gsize; i++)
+    {
+      hseqs[index++] = sg.getSequenceAt(i);
+    }
+
+    ap.av.hideSequence(hseqs);
+  }
+
+  public void copy_actionPerformed()
+  {
+    ap.alignFrame.copy_actionPerformed(null);
+  }
+
+  public void cut_actionPerformed()
+  {
+    ap.alignFrame.cut_actionPerformed(null);
+  }
+
+  void changeCase(ActionEvent e)
+  {
+    Object source = e.getSource();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+          sg.getStartRes(), sg.getEndRes() + 1);
+
+      String description;
+      int caseChange;
+
+      if (source == toggle)
+      {
+        description = "Toggle Case";
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;
+      }
+      else if (source == upperCase)
+      {
+        description = "To Upper Case";
+        caseChange = ChangeCaseCommand.TO_UPPER;
+      }
+      else
+      {
+        description = "To Lower Case";
+        caseChange = ChangeCaseCommand.TO_LOWER;
+      }
+
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
+          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+          startEnd, caseChange
+          );
+
+      ap.alignFrame.addHistoryItem(caseCommand);
+
+      ap.av.firePropertyChange("alignment", null,
+                               ap.av.getAlignment().getSequences());
+
+    }
+  }
+
+  public void outputText_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
+
+    String[] omitHidden = null;
+
+    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
+    omitHidden = ap.av.getViewAsString(true);
+    Alignment oal = new Alignment(ap.av.getSequenceSelection());
+    AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+    for (int i=0; i<nala.length; i++)
+    {
+      AlignmentAnnotation na =nala[i];
+      oal.addAnnotation(na);
+    }
+    cap.setText(new FormatAdapter().formatSequences(
+            e.getActionCommand(),
+            oal,
+            omitHidden, csel, sg));
+    oal=null;
+  }
+
+  public void pdbFromFile_actionPerformed()
+  {
+    jalview.io.JalviewFileChooser chooser
+        = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
+                                            getProperty(
+                                                "LAST_DIRECTORY"));
+    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setDialogTitle("Select a PDB file");
+    chooser.setToolTipText("Load a PDB file");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    {
+      PDBEntry entry = new PDBEntry();
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      try
+      {
+        MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+            jalview.io.AppletFormatAdapter.FILE);
+
+        if (pdbfile.id == null)
+        {
+          String reply = JOptionPane.showInternalInputDialog(
+              Desktop.desktop,
+              "Couldn't find a PDB id in the file supplied."
+              + "Please enter an Id to identify this structure.",
+              "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+          if (reply == null)
+          {
+            return;
+          }
+
+          entry.setId(reply);
+        }
+        else
+        {
+          entry.setId(pdbfile.id);
+        }
+      }
+      catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+
+      entry.setFile(choice);
+      sequence.getDatasetSequence().addPDBId(entry);
+    }
+
+  }
+
+  public void enterPDB_actionPerformed()
+  {
+    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+    if (id != null && id.length() > 0)
+    {
+      PDBEntry entry = new PDBEntry();
+      entry.setId(id.toUpperCase());
+      sequence.getDatasetSequence()
+          .addPDBId(entry);
+    }
+  }
+
+  public void discoverPDB_actionPerformed()
+  {
+    
+    final SequenceI[] sequences = 
+      ((ap.av.selectionGroup == null) 
+              ?  new Sequence[]{sequence}
+      : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+    Thread discpdb = new Thread(new Runnable() {
+      public void run()
+      {
+        
+        new jalview.ws.DBRefFetcher(sequences,
+                ap.alignFrame).fetchDBRefs(false);
+      }
+      
+    });
+    discpdb.start();
+  }
+
+  public void sequenceFeature_actionPerformed()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null)
+    {
+      return;
+    }
+
+    int gSize = sg.getSize();
+    SequenceI[] seqs = new SequenceI[gSize];
+    SequenceFeature[] features = new SequenceFeature[gSize];
+
+    for (int i = 0; i < gSize; i++)
+    {
+      seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+      int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+      int end = sg.findEndRes(sg.getSequenceAt(i));
+      features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
+    }
+
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .amendFeatures(seqs, features, true, ap))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
+
+  public void textColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg != null)
+    {
+      new TextColourChooser().chooseColour(ap, sg);
+    }
+  }
+
+  public void colourByStructure(String pdbid)
+  {
+    Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+        .colourSequenceFromStructure(sequence, pdbid);
+
+    AlignmentAnnotation an = new AlignmentAnnotation(
+      "Structure", "Coloured by "+pdbid, anots);
+
+    ap.av.alignment.addAnnotation(an);
+    an.createSequenceMapping(sequence, 0, true);
+    //an.adjustForAlignment();
+    ap.av.alignment.setAnnotationIndex(an,0);
+
+    ap.adjustAnnotationHeight();
+
+    sequence.addAlignmentAnnotation(an);
+
+    }
+
+  public void editSequence_actionPerformed(ActionEvent actionEvent)
+  {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+
+      if(sg!=null)
+      {
+        if (sequence == null)
+          sequence = (Sequence) sg.getSequenceAt(0);
+
+        EditNameDialog dialog = new EditNameDialog(
+            sequence.getSequenceAsString(
+                sg.getStartRes(),
+                sg.getEndRes() + 1),
+            null,
+            "Edit Sequence ",
+            null,
+            "Edit Sequence");
+
+        if (dialog.accept)
+        {
+          EditCommand editCommand = new EditCommand(
+              "Edit Sequences", EditCommand.REPLACE,
+              dialog.getName().replace(' ', ap.av.getGapCharacter()),
+              sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+              sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
+              );
+
+          ap.alignFrame.addHistoryItem(editCommand);
+
+          ap.av.firePropertyChange("alignment", null,
+                                   ap.av.getAlignment().getSequences());
+        }
+      }
+  }
+
+
+}