X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=206a969d106b2993521607c4f7883fdad9e01701;hb=f62b380e6e3cdbce3af5730f682aad99116509c9;hp=458a6bed4315767e275700518d6b8e1a3650e82c;hpb=f44e5d441ae27d834b3a5096060ac8b5df5c5c9c;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 458a6be..206a969 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,526 +1,1445 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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 jalview.datamodel.*;
+import MCview.*;
+
 import jalview.analysis.*;
+import jalview.datamodel.*;
 import jalview.schemes.*;
-import javax.swing.*;
+import jalview.commands.ChangeCaseCommand;
+
+import java.awt.*;
 import java.awt.event.*;
 
+import javax.swing.*;
+
+import java.util.Vector;
+import jalview.io.FormatAdapter;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.ChangeEvent;
+
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class PopupMenu extends JPopupMenu
 {
-  JMenuItem residueMenu = new JMenuItem();
-  JMenu groupMenu = new JMenu();
-  JMenuItem copyGroup = new JMenuItem();
-  JMenuItem moveGroup = new JMenuItem();
-  JMenuItem deleteSequences = new JMenuItem();
-  JMenuItem analyze = new JMenuItem();
-  JMenu defineMenu = new JMenu();
-  JMenuItem groupName = new JMenuItem();
-  JMenuItem groupAnnotation = 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 JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-  protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
-
-  AlignViewport av;
-  SeqPanel seqPanel;
-
-  public PopupMenu(AlignViewport av, SeqPanel sp)
-  {
-    this.av = av;
-    seqPanel = sp;
-
-    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)
+    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();
+
+  /**
+     * Creates a new PopupMenu object.
+     *
+     * @param ap DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
     {
-      e.printStackTrace();
+        ///////////////////////////////////////////////////////////
+        // 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)
+          {
+            java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+                elements();
+
+            while (e.hasMoreElements())
+            {
+              final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+              menuItem = new JMenuItem();
+              menuItem.setText("View PDB entry: " + pdb.getId());
+              menuItem.addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(ActionEvent e)
+                {
+                  new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
+                }
+              });
+              sequenceMenu.add(menuItem);
+            }
+          }
+
+          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(false)>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);
+            pdbMenu.setVisible(false);
+        }
+
+        if(links != null && links.size()>0)
+        {
+          JMenu linkMenu = new JMenu("Link");
+          JMenuItem item;
+          for(int i=0; i<links.size(); i++)
+          {
+            String link = links.elementAt(i).toString();
+            final String label = link.substring(0, link.indexOf("|"));
+            item = new JMenuItem(label);
+            final String url;
+
+            if (link.indexOf("$SEQUENCE_ID$") > -1)
+            {
+              String id = seq.getName();
+              if (id.indexOf("|") > -1)
+                id = id.substring(id.lastIndexOf("|") + 1);
+
+              url = link.substring(link.indexOf("|") + 1,
+                                   link.indexOf("$SEQUENCE_ID$"))
+                  + id +
+                  link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+            }
+            else
+              url = link.substring(link.lastIndexOf("|")+1);
+
+
+            item.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    showLink(url);
+                }
+            });
+
+            linkMenu.add(item);
+          }
+          if(sequence!=null)
+            sequenceMenu.add(linkMenu);
+          else
+            add(linkMenu);
+        }
     }
 
-    SequenceGroup sg = av.getRubberbandGroup();
-    groupName.setText( sg.getName() );
-  }
-  private void jbInit() throws Exception
-  {
-    residueMenu.setText("Residue");
-    groupMenu.setText("Group");
-    copyGroup.setText("Copy region to new Alignment");
-    copyGroup.addActionListener(new java.awt.event.ActionListener()
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        copyGroup_actionPerformed(e);
-      }
-    });
-    moveGroup.setText("Move sequences to new Alignment");
-    moveGroup.addActionListener(new java.awt.event.ActionListener()
+        groupMenu.setText("Group");
+        groupMenu.setText("Selection");
+        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/Description");
+        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);
+                }
+            });
+
+        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);
+                }
+            });
+    editMenu.setText("Edit");
+    cut.setText("Cut");
+    cut.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        moveGroup_actionPerformed(e);
+        cut_actionPerformed(e);
       }
     });
-    deleteSequences.setText("Delete sequences");
-    deleteSequences.addActionListener(new java.awt.event.ActionListener()
+    upperCase.setText("To Upper Case");
+    upperCase.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        deleteSequences_actionPerformed(e);
+        changeCase(e);
       }
     });
-    analyze.setText("Analyze");
-    analyze.addActionListener(new java.awt.event.ActionListener()
+    copy.setText("Copy");
+    copy.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        analyze_actionPerformed(e);
+        copy_actionPerformed(e);
       }
     });
-    defineMenu.setText("Define");
-    groupName.setText("Name");
-    groupName.addActionListener(new java.awt.event.ActionListener()
+    lowerCase.setText("To Lower Case");
+    lowerCase.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        groupName_actionPerformed(e);
+        changeCase(e);
       }
     });
-    groupAnnotation.setText("Annotation");
-    groupAnnotation.addActionListener(new java.awt.event.ActionListener()
+    toggle.setText("Toggle Case");
+    toggle.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        groupAnnotation_actionPerformed(e);
+        changeCase(e);
       }
     });
-    add(groupMenu);
-    add(residueMenu);
-    groupMenu.add(defineMenu);
-    groupMenu.addSeparator();
-    groupMenu.add(copyGroup);
-    groupMenu.add(moveGroup);
-    groupMenu.add(deleteSequences);
-    groupMenu.addSeparator();
-    groupMenu.add(analyze);
-    defineMenu.add(groupName);
-    defineMenu.add(groupAnnotation);
-    defineMenu.addSeparator();
-    defineMenu.add(noColourmenuItem);
-    defineMenu.add(clustalColour);
-    defineMenu.add(zappoColour);
-    defineMenu.add(taylorColour);
-    defineMenu.add(hydrophobicityColour);
-    defineMenu.add(helixColour);
-    defineMenu.add(strandColour);
-    defineMenu.add(turnColour);
-    defineMenu.add(buriedColour);
-    defineMenu.add(userDefinedColour);
-    defineMenu.addSeparator();
-    defineMenu.add(conservationMenuItem);
-    defineMenu.add(conservationColourIncMenuItem);
-    defineMenu.addSeparator();
-    defineMenu.add(abovePIDColour);
-    defineMenu.add(PIDColour);
-    defineMenu.add(BLOSUM62Colour);
-
-    noColourmenuItem.setText("None");
-    noColourmenuItem.setSelected(true);
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    pdbMenu.setText("Associate Structure with Sequence");
+    pdbFromFile.setText("From File");
+    pdbFromFile.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        noColourmenuItem_actionPerformed(e);
+        pdbFromFile_actionPerformed(e);
       }
     });
-
-    clustalColour.setEnabled(false);
-    clustalColour.setSelected(false);
-    clustalColour.setText("Clustalx colours");
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    enterPDB.setText("Enter PDB Id");
+    enterPDB.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        clustalColour_actionPerformed(e);
+        enterPDB_actionPerformed(e);
       }
     });
-    zappoColour.setText("Zappo colour scheme");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    discoverPDB.setText("Discover PDB ids");
+    discoverPDB.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        zappoColour_actionPerformed(e);
+        discoverPDB_actionPerformed(e);
       }
     });
-    taylorColour.setText("Taylor colour scheme");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        taylorColour_actionPerformed(e);
+        sequenceFeature_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText("By hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        hydrophobicityColour_actionPerformed(e);
+        textColour_actionPerformed(e);
       }
     });
-    helixColour.setText("Helix propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
+    jMenu1.setText("Group");
+    add(groupMenu);
+
+    add(sequenceMenu);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputMenu);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(jMenu1);
+    sequenceMenu.add(sequenceName);
+    sequenceMenu.add(pdbMenu);
+    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);
+    editMenu.add(copy);
+    editMenu.add(cut);
+    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);
+    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()
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed(e);
-      }
-    });
-    strandColour.setText("Strand propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
+        if (ap.overviewPanel != null)
+          ap.overviewPanel.updateOverviewImage();
+
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void clustalColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed(e);
-      }
-    });
-    turnColour.setText("Turn propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
+        SequenceGroup sg = getGroup();
+        sg.cs = new ClustalxColourScheme(sg.getSequences(true),
+                ap.av.alignment.getWidth());
+        refresh();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void zappoColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed(e);
-      }
-    });
-    buriedColour.setText("Buried index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
+        getGroup().cs = new ZappoColourScheme();
+        refresh();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void taylorColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed(e);
-      }
-    });
-    abovePIDColour.setEnabled(false);
-    abovePIDColour.setText("Above PID threshold only");
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+        getGroup().cs = new TaylorColourScheme();
+        refresh();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void hydrophobicityColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDColour_actionPerformed(e);
-      }
-    });
-    userDefinedColour.setText("User defined colours");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+        getGroup().cs = new HydrophobicColourScheme();
+        refresh();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void helixColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
-    PIDColour.setEnabled(false);
-    PIDColour.setText("By PID");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
+        getGroup().cs = new HelixColourScheme();
+        refresh();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void strandColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed(e);
-      }
-    });
-    BLOSUM62Colour.setText("By BLOSUM62 score");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+        getGroup().cs = new StrandColourScheme();
+        refresh();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void turnColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed(e);
-      }
-    });
-    conservationMenuItem.setText("By conservation");
-   conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-   {
-     public void actionPerformed(ActionEvent e)
-     {
-       conservationMenuItem_actionPerformed(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.getSequences(true), 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(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
+        sg.cs = new PIDColourScheme();
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
+        refresh();
+    }
 
-    conservationColourIncMenuItem.setEnabled(false);
-    conservationColourIncMenuItem.setText("Conservation Colour Increment");
-    conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationColourIncMenuItem_actionPerformed(e);
-      }
-    });
+        SequenceGroup sg = getGroup();
 
+        sg.cs = new Blosum62ColourScheme();
 
-  }
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
 
-  void refresh()
-  {
-    seqPanel.seqCanvas.paintFlag=true;
-    seqPanel.repaint();
-  }
+        refresh();
+    }
 
-  protected void clustalColour_actionPerformed(ActionEvent e)
-  {
+    /**
+     * 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.getSequences(true),
+                    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();
+    }
 
-  protected void zappoColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new ZappoColourScheme();
-    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);
+    }
 
-  protected void taylorColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new TaylorColourScheme();
-    refresh();
-  }
 
+    /**
+     * 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);
 
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new HydrophobicColourScheme();
-    refresh();
-  }
+        return sg;
+    }
 
-  protected void helixColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new HelixColourScheme();
-    refresh();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    void sequenceName_actionPerformed(ActionEvent e)
+    {
+      JLabel idlabel = new JLabel(  "       Sequence Name ");
+      JLabel desclabel = new JLabel("Sequence Description ");
+      idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
+      desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
+      JTextField id = new JTextField(sequence.getName(), 40);
+      JTextField description = new JTextField(sequence.getDescription(), 40);
+      JPanel panel = new JPanel(new BorderLayout());
+      JPanel panel2 = new JPanel(new BorderLayout());
+      panel2.add(idlabel, BorderLayout.WEST);
+      panel2.add(id, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.NORTH);
+      panel2 = new JPanel(new BorderLayout());
+      panel2.add(desclabel, BorderLayout.WEST);
+      panel2.add(description, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.SOUTH);
+
+
+       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          panel, "Edit Sequence Name/Description",
+          JOptionPane.OK_CANCEL_OPTION );
+
+
+        if (reply != JOptionPane.OK_OPTION )
+        {
+            return;
+        }
+
+        String s = id.getText();
+
+        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();
+        }
+
+        sequence.setDescription(description.getText());
+
+        ap.av.firePropertyChange("alignment", null,
+                                  ap.av.getAlignment().getSequences());
 
-  protected void strandColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new StrandColourScheme();
-    refresh();
-  }
+    }
 
-  protected void turnColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new TurnColourScheme();
-    refresh();
-  }
+    /**
+     * 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();
+    }
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new BuriedColourScheme();
-    refresh();
-  }
 
+    /**
+     * 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);
 
-  protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
- {
+        if (col != null)
+        {
+            sg.setOutlineColour(col);
+        }
 
-}
-/*
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
-{
-ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
-JInternalFrame frame = new JInternalFrame();
-frame.setContentPane(cip);
-Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
-frame.setMaximizable(false);
+        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();
+    }
 
-  protected void abovePIDColour_actionPerformed(ActionEvent e)
-  {
+    /**
+     * 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 );
 
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, seqPanel.parent, getGroup());
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+        ex.printStackTrace();
+      }
+    }
 
-  }
+    void hideSequences(boolean representGroup)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if(sg==null || sg.getSize(false)<1)
+      {
+        ap.av.hideSequence(new SequenceI[]{sequence});
+        return;
+      }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
+      int gsize = sg.getSize(false);
+      SequenceI [] hseqs;
 
-  }
+      hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
+
+        int index = 0;
+        for(int i=0; i<gsize; i++)
+        {
+          if(representGroup && sg.getSequenceAt(i)!=sequence)
+          {
+            sequence.addHiddenSequence(sg.getSequenceAt(i));
+            hseqs[index++] = sg.getSequenceAt(i);
+          }
+          else if(!representGroup)
+          {
+            hseqs[index++] = sg.getSequenceAt(i);
+          }
+        }
+
+        ap.av.hideSequence(hseqs);
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+        ap.av.setSelectionGroup(null);
+    }
+
+  public void copy_actionPerformed(ActionEvent e)
   {
-    getGroup().cs = new Blosum62ColourScheme(av);
-    refresh();
+    ap.alignFrame.copy_actionPerformed(null);
   }
 
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  public void cut_actionPerformed(ActionEvent e)
   {
-    getGroup().cs = null;
-    refresh();
+    ap.alignFrame.cut_actionPerformed(null);
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  void changeCase(ActionEvent e)
   {
-    SequenceGroup sg = getGroup();
+    Object source = e.getSource();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    Vector regions = new Vector();
+    if (sg != null)
+    {
+      int start = sg.getStartRes();
+      int end = sg.getEndRes() + 1;
 
-    Conservation c = new Conservation("Group",
-                          ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),
-                          sg.getEndRes() );
+      do
+      {
+        if (ap.av.hasHiddenColumns)
+        {
+          if(start==0)
+            start = ap.av.colSel.adjustForHiddenColumns(start);
+
+          end = ap.av.colSel.getHiddenBoundaryRight(start);
+          if (start == end)
+            end = sg.getEndRes() + 1;
+          if (end > sg.getEndRes())
+            end = sg.getEndRes() + 1;
+        }
+
+        regions.addElement(new int[]
+                           {start, end});
+
+        if (ap.av.hasHiddenColumns)
+        {
+          start = ap.av.colSel.adjustForHiddenColumns(end);
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+        }
+      }
+      while (end < sg.getEndRes());
 
-     c.calculate();
-     c.verdict(false, 100);
-     ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+      int[][] startEnd = new int[regions.size()][2];
+      for (int i = 0; i < regions.size(); i++)
+      {
+        startEnd[i] = (int[]) regions.elementAt(i);
+      }
 
-     sg.cs = ccs;
 
-     refresh();
-  }
+      String description;
+      int caseChange;
 
-  protected void groupAnnotation_actionPerformed(ActionEvent e)
-  {
+      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(true), startEnd, caseChange
+          );
 
-  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;
+      ap.alignFrame.addHistoryItem(caseCommand);
 
-    sg.setName(reply);
-    groupName.setText(reply);
-  }
-  /*  public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
-    {
-      addHistoryItem("delete selection");
 
-      for (int i=0;i < viewport.getSelection().size(); i++)
-              viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
+      ap.av.firePropertyChange("alignment", null,
+                                ap.av.getAlignment().getSequences());
 
-      viewport.getSelection().clear();
-      viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
-      alignPanel.RefreshPanels();
     }
+  }
+
+  public void outputText_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
 
-    public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
+    String [] omitHidden = null;
+
+    if(ap.av.hasHiddenColumns)
     {
-      copySelectedMenuItem_actionPerformed(null);
-      deleteSelectedMenuItem_actionPerformed(null);
-      alignPanel.repaint();
+      System.out.println("PROMPT USER HERE");
+      omitHidden = ap.av.getViewAsString(true);
     }
 
-    public void copySelectedMenuItem_actionPerformed(ActionEvent e)
-    {
-      if(viewport.getSelection().size()==0)
-        return;
+    cap.setText(new FormatAdapter().formatSequences(
+        e.getActionCommand(),
+        ap.av.getSelectionAsNewSequence(),
+        omitHidden));
+  }
 
-     SequenceI[] s = new Sequence[viewport.getSelection().size()];
-     for (int i=0; i < viewport.getSelection().size(); i++) {
-       s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
-      }
-      AlignFrame af = new AlignFrame(new Alignment(s));
-      int newHeight = s.length * af.viewport.getCharHeight() + 200;
-      if(newHeight>500)
-        newHeight=500;
-      Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
-    }
-*/
-  protected void copyGroup_actionPerformed(ActionEvent e)
+
+  public void pdbFromFile_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = av.getRubberbandGroup();
+     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);
 
-    SequenceI[] s = new Sequence[sg.sequences.size()];
-     for (int i=0; i < sg.sequences.size(); i++)
+     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
      {
-       s[i] = new Sequence( sg.getSequenceAt(i));
-       s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
+       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);
      }
-     AlignFrame af = new AlignFrame(new Alignment(s));
-     int newHeight = s.length * af.viewport.getCharHeight() + 200;
-     if (newHeight > 500)
-       newHeight = 500;
-     Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
+
   }
 
-  protected  void moveGroup_actionPerformed(ActionEvent e)
+  public void enterPDB_actionPerformed(ActionEvent e)
   {
+    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);
+      sequence.getDatasetSequence()
+          .addPDBId(entry);
+    }
   }
 
-  protected void deleteSequences_actionPerformed(ActionEvent e)
+  public void discoverPDB_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = av.getRubberbandGroup();
-    for (int i=0;i < sg.sequences.size(); i++)
-            av.getAlignment().deleteSequence(sg.getSequenceAt(i));
-
-    av.alignment.deleteGroup(sg);
-    av.resetSeqLimits(seqPanel.seqCanvas.getHeight());
-    seqPanel.parent.RefreshPanels();
-
+    new jalview.io.DBRefFetcher(
+             ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
   }
 
-  protected void analyze_actionPerformed(ActionEvent e)
+  public void sequenceFeature_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     JInternalFrame frame = new JInternalFrame();
-     cap.formatForOutput();
-     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");
-     }
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    int gSize= sg.getSize(false);
+    SequenceI [] seqs = new SequenceI[gSize];
+    SequenceFeature [] features = new SequenceFeature[gSize];
 
-     sb.append("Something amazing will happen soon");
-     cap.setText( sb.toString() );
+    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()
+        .createNewFeatures(seqs, features))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
   }
 
-  SequenceGroup getGroup()
+  public void textColour_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = av.getRubberbandGroup();
+    final SequenceGroup sg = getGroup();
+
+    int original1 = sg.textColour.getRGB();
+    int original2 = sg.textColour2.getRGB();
+    int thresh = sg.thresholdTextColour;
+    final JSlider slider = new JSlider(0, 750,sg.thresholdTextColour);
+    final JButton col1 = new JButton("DARK");
+    col1.setBackground(sg.textColour);
+    col1.setForeground(sg.textColour);
+    final JButton col2 = new JButton("LIGHT");
+    col2.setBackground(sg.textColour2);
+    col2.setForeground(sg.textColour2);
+    final JPanel bigpanel = new JPanel(new BorderLayout());
+    JPanel panel = new JPanel();
+    bigpanel.add(panel, BorderLayout.CENTER);
+    bigpanel.add(new JLabel(
+      "<html><i>Select a dark and light text colour, then set the threshold to"
+     +"<br>switch between colours, based on background colour</i></html>"),
+                 BorderLayout.NORTH);
+    panel.add(col1);
+    panel.add(slider);
+    panel.add(col2);
+
+    col1.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            Color col = JColorChooser.showDialog(bigpanel,
+                                                 "Select Colour for Text",
+                                                 sg.textColour);
+            if (col != null)
+            {
+              sg.textColour = col;
+              col1.setBackground(col);
+              col1.setForeground(col);
+            }
+            ap.repaint();
+          }
+        });
+
+    col2.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        Color col = JColorChooser.showDialog(bigpanel,
+                                             "Select Colour for Text",
+                                             sg.textColour);
+        if (col != null)
+        {
+          sg.textColour2 = col;
+          col2.setBackground(col);
+          col2.setForeground(col);
+        }
+        ap.repaint();
+      }
+    });
 
-    // this method won't add a new group if it already exists
-    av.alignment.addGroup(sg);
-    return sg;
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        sg.thresholdTextColour = slider.getValue();
+        ap.repaint();
+      }
+    });
+
+    int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+                                                 bigpanel,
+                                                 "Adjust Foreground Text Colour Threshold",
+                                                 JOptionPane.OK_CANCEL_OPTION,
+                                                 JOptionPane.QUESTION_MESSAGE,
+                                                 null,
+                                                 null, null);
+
+    if(reply==JOptionPane.CANCEL_OPTION)
+    {
+      sg.textColour = new Color(original1);
+      sg.textColour2 = new Color(original2);
+      sg.thresholdTextColour = thresh;
+    }
   }
 }