X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1377de2b1fef0fab631c3e63a3efced38ca90076;hb=783520af519c958e10a2af29f1d4242e1ab890a3;hp=62d69d00aa38ecb2e5ec035bb4741478894afd08;hpb=714aae012ecf6cb27e602eaafdb6458b885dc80c;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 62d69d0..1377de2 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,552 +1,934 @@
+/*
+ * 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 jalview.datamodel.*;
+import MCview.*;
+
 import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
 import jalview.schemes.*;
-import javax.swing.*;
+
+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 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 JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
-
-  AlignmentPanel ap;
-  JMenu sequenceMenu = new JMenu();
-  JMenuItem sequenceName = new JMenuItem();
-  JMenu residueMenu = new JMenu();
-  JMenuItem annotateResidue = new JMenuItem();
-
-  SequenceI sequence;
-
-  public PopupMenu(AlignmentPanel ap, SequenceI 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();    }
-
-    SequenceGroup sg = ap.av.getRubberbandGroup();
-    if(sg!=null)
-      groupName.setText( sg.getName() );
-
-    if(seq!=null)
+    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)
     {
-      residueMenu.setVisible(false);
-      sequenceName.setText( sequence.getName() );
+        ///////////////////////////////////////////////////////////
+        // 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);
+        }
     }
-    else
-      sequenceMenu.setVisible(false);
-
-  }
-  private void jbInit() throws Exception
-  {
-    groupMenu.setText("Group");
-    copyGroup.setText("Copy region to new Alignment");
-    copyGroup.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        copyGroup_actionPerformed(e);
-      }
-    });
-    moveGroup.setText("Move sequences to new Alignment");
-    moveGroup.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        moveGroup_actionPerformed(e);
-      }
-    });
-    deleteSequences.setText("Delete sequences");
-    deleteSequences.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deleteSequences_actionPerformed(e);
-      }
-    });
-    analyze.setText("Analyze");
-    analyze.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        analyze_actionPerformed(e);
-      }
-    });
-    defineMenu.setText("Define");
-    groupName.setText("Name");
-    groupName.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        groupName_actionPerformed(e);
-      }
-    });
-    groupAnnotation.setText("Annotation");
-    groupAnnotation.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        groupAnnotation_actionPerformed(e);
-      }
-    });
-    sequenceMenu.setText("Sequence");
-    sequenceName.setText("sequenceName");
-    sequenceName.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sequenceName_actionPerformed(e);
-      }
-    });
-    residueMenu.setText("Residue");
-    annotateResidue.setText("annotate residue???");
-    PIDColour.setFocusPainted(false);
-    add(groupMenu);
-    this.add(sequenceMenu);
-    this.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.add(PIDColour);
-    defineMenu.add(BLOSUM62Colour);
-    defineMenu.addSeparator();
-    defineMenu.add(abovePIDColour);
-    defineMenu.add(conservationMenuItem);
-
-    sequenceMenu.add(sequenceName);
-    residueMenu.add(annotateResidue);
-
-    noColourmenuItem.setText("None");
-    noColourmenuItem.setSelected(true);
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        noColourmenuItem_actionPerformed(e);
-      }
-    });
 
-    clustalColour.setSelected(false);
-    clustalColour.setText("Clustalx colours");
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed(e);
-      }
-    });
-    zappoColour.setText("Zappo colour scheme");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed(e);
-      }
-    });
-    taylorColour.setText("Taylor colour scheme");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed(e);
-      }
-    });
-    hydrophobicityColour.setText("By 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 PID threshold only");
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDColour_actionPerformed(e);
-      }
-    });
-    userDefinedColour.setText("User defined colours");
-    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 score");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
-    {
-      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);
-     }
-   });
-
-
-
-  }
-
-  void refresh()
-  {
-    ap.seqPanel.seqCanvas.paintFlag=true;
-    ap.seqPanel.repaint();
-  }
-
-  protected void clustalColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new ClustalxColourScheme();
-    refresh();
-  }
-
-  protected void zappoColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new ZappoColourScheme();
-    refresh();
-  }
-
-  protected void taylorColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new TaylorColourScheme();
-    refresh();
-  }
-
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new HydrophobicColourScheme();
-    refresh();
-  }
-
-  protected void helixColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new HelixColourScheme();
-    refresh();
-  }
-
-  protected void strandColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new StrandColourScheme();
-    refresh();
-  }
-
-  protected void turnColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new TurnColourScheme();
-    refresh();
-  }
-
-  protected void buriedColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new BuriedColourScheme();
-    refresh();
-  }
-
-
-/*
-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);
-
- }*/
-
-
-  protected void abovePIDColour_actionPerformed(ActionEvent e)
-  {
-    SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400,90);
-    frame.setMaximizable(false);
-
-  }
+        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();
+    }
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+    /**
+     * 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();
+    }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
+    /**
+     * 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();
+    }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new Blosum62ColourScheme(ap.av);
-    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();
+    }
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = null;
-    refresh();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void turnColour_actionPerformed(ActionEvent e)
+    {
+        getGroup().cs = new TurnColourScheme();
+        refresh();
+    }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void buriedColour_actionPerformed(ActionEvent e)
+    {
+        getGroup().cs = new BuriedColourScheme();
+        refresh();
+    }
 
-    Conservation c = new Conservation("Group",
-                          ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),
-                          sg.getEndRes() );
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void nucleotideMenuItem_actionPerformed(ActionEvent e)
+    {
+        getGroup().cs = new NucleotideColourScheme();
+        refresh();
+    }
 
-     c.calculate();
-     c.verdict(false, 100);
-     ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void abovePIDColour_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
-     sg.cs = ccs;
+        if (abovePIDColour.isSelected())
+        {
+            sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                    ap.av.alignment.getWidth()));
 
-     refresh();
-  }
+            int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+                    getGroup().getName());
 
-  protected void groupAnnotation_actionPerformed(ActionEvent e)
-  {
+           sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
-  }
+            SliderPanel.showPIDSlider();
+        }
+        else // remove PIDColouring
+        {
+            sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+        }
 
-  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;
+        refresh();
+    }
 
-    sg.setName(reply);
-    groupName.setText(reply);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void userDefinedColour_actionPerformed(ActionEvent e)
+    {
+       SequenceGroup sg = getGroup();
 
-  protected void copyGroup_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
+       if (e.getActionCommand().equals("User Defined..."))
+         new UserDefinedColours(ap, sg);
+       else
+       {
+         UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+             getUserColourSchemes().get(e.getActionCommand());
 
-    SequenceI[] s = new Sequence[sg.sequences.size()];
-     for (int i=0; i < sg.sequences.size(); i++)
-     {
-       s[i] = new Sequence( sg.getSequenceAt(i));
-       s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
+         sg.cs = udc;
+       }
      }
-     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)
-  {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
-
-    SequenceI[] s = new Sequence[sg.sequences.size()];
+    /**
+     * 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();
+    }
 
-     for (int i=0; i < sg.sequences.size(); i++)
-       s[i] = new Sequence( sg.getSequenceAt(i));
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
 
-     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);
+        sg.cs = new Blosum62ColourScheme();
 
+        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                ap.av.alignment.getWidth()));
 
-     for (int i=0; i < sg.sequences.size(); i++)
-       ap.av.alignment.deleteSequence(sg.getSequenceAt(i));
+        refresh();
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void noColourmenuItem_actionPerformed(ActionEvent e)
+    {
+        getGroup().cs = null;
+        refresh();
+    }
 
-     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
-     ap.RefreshPanels();
+    /**
+     * 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());
+    }
 
-  protected void deleteSequences_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
-    for (int i=0;i < sg.sequences.size(); i++)
-            ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));
+    /**
+     * 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);
 
-    ap.av.alignment.deleteGroup(sg);
-    ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
-    ap.seqPanel.parent.RefreshPanels();
+        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();
+        }
+    }
 
-  protected void analyze_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();
+    /**
+     * 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();
+    }
 
-     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");
-     }
+    /**
+     * 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();
+        }
+    }
 
-     sb.append("Something amazing will happen soon");
-     cap.setText( sb.toString() );
+    /**
+     * 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);
+        }
 
-  SequenceGroup getGroup()
-  {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
+        refresh();
+    }
 
-    // this method won't add a new group if it already exists
-    ap.av.alignment.addGroup(sg);
-    return sg;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void showBoxes_actionPerformed(ActionEvent e)
+    {
+        getGroup().setDisplayBoxes(showBoxes.isSelected());
+        refresh();
+    }
 
-  void sequenceName_actionPerformed(ActionEvent e)
-  {
-    String id = sequence.getName();
-    String s = (String)JOptionPane.showInternalInputDialog(
-                ap,
-                "Edit sequence name",
-                "Edit sequence name",
-                JOptionPane.PLAIN_MESSAGE,
-                null,
-                null,
-                id);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void showText_actionPerformed(ActionEvent e)
+    {
+        getGroup().setDisplayText(showText.isSelected());
+        refresh();
+    }
 
-    if(s!=null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void showColourText_actionPerformed(ActionEvent e)
     {
-      sequence.setName(s);
-      ap.RefreshPanels();
+        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();
+      }
+    }
 }