X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=01a0907133eeff856355f6b671caecf596b52e86;hb=68a07ae7d499ec6d176cd246bc9060956bd40fa7;hp=19698b7f13495587fd2b9c5f44b9c2f5f2b81fdc;hpb=ff3c6d412fe13784cde1e15a12567d6537f4151c;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 19698b7..01a0907 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,793 +1,1493 @@
-package jalview.gui;
-
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
-import javax.swing.*;
-import java.awt.event.*;
-
-
-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 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();
-  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(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 instanceof ConservationColourScheme)
-        conservationMenuItem.setSelected(true);
-
-    }
-
-    if(seq!=null)
-    {
-      residueMenu.setVisible(false);
-      sequenceName.setText( sequence.getName() );
-    }
-    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.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 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()
-    {
-      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 ("+getGroup().getName()+")" , 400,90);
-    frame.setMaximizable(false);
-
-  }
-
-
-  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 ("+getGroup().getName()+")", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
-
-  }
-
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new Blosum62ColourScheme(ap.av);
-    refresh();
-  }
-
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = null;
-    refresh();
-  }
-
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-
-    Conservation c = new Conservation("Group",
-                          ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),
-                          sg.getEndRes() );
-
-     c.calculate();
-     c.verdict(false, 100);
-     ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-     sg.cs = ccs;
-
-     refresh();
-  }
-
-/*
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( null );
-    changeColour();
-  }
-
-
-  public void clustalColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
-    conservationMenuItem.setSelected(false);
-    abovePIDThreshold.setSelected(false);
-    changeColour();
-  }
-
-  public void zappoColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new ZappoColourScheme() );
-    changeColour();
-  }
-
-  public void taylorColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new TaylorColourScheme() );
-    changeColour();
-  }
-
-
-  public void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
-    changeColour();
-  }
-
-  public void helixColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new HelixColourScheme()  );
-    changeColour();
-  }
-
-
-  public void strandColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new StrandColourScheme() );
-    changeColour();
-  }
-
-
-  public void turnColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new TurnColourScheme() );
-    changeColour();
-  }
-
-
-  public void buriedColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new BuriedColourScheme() );
-    changeColour();
-  }
-
-  void changeColour()
-  {
-    if(abovePIDThreshold.isSelected())
-      abovePIDThreshold_actionPerformed(null);
-    else if(conservationMenuItem.isSelected())
-      conservationMenuItem_actionPerformed(null);
-
-     alignPanel.seqPanel.seqCanvas.paintFlag = true;
-     alignPanel.repaint();
-  }
-
-  void addConservationOrPIDColour()
-  {
-    int x=0, y=0, threshold = 70;
-
-    if(sliderFrame!=null)
-       try
-       {
-         x = sliderFrame.getX();
-         y = sliderFrame.getY();
-         SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
-         threshold = sp.getValue();
-         sliderFrame.setClosed(true);
-       }
-       catch (Exception ex)
-       {    ex.printStackTrace();   }
-
-     ColourSchemeI oldCs = viewport.getGlobalColourScheme();
-
-     ConservationColourScheme ccs = null;
-     if (oldCs instanceof ConservationColourScheme)
-       ccs = (ConservationColourScheme) oldCs;
-
-     if(conservationMenuItem.isSelected())
-     {
-       Alignment al = (Alignment)viewport.alignment;
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
-
-       c.calculate();
-       c.verdict(false, 100);
-
-       if(ccs!=null)
-         ccs = new ConservationColourScheme(c, ccs.cs);
-       else
-         ccs = new ConservationColourScheme(c, oldCs);
-
-        viewport.setGlobalColourScheme( ccs );
-
-     }
-     else if(oldCs instanceof ConservationColourScheme)
-     {
-       oldCs = ccs.cs;
-       viewport.setGlobalColourScheme( oldCs );
-     }
-
-
-     if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
-     {
-       sliderFrame = new JInternalFrame();
-       sliderFrame.setMaximizable(false);
-       sliderFrame.setResizable(false);
-
-       SliderPanel sp = null;
-       if (conservationMenuItem.isSelected())
-       {
-        if(threshold > 50)
-          threshold = 30;
-        sp = new SliderPanel(alignPanel, threshold, true,ccs);
-        Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);
-        threshold = 0;
-       }
-       else if (abovePIDThreshold.isSelected())
-       {
-         sp = new SliderPanel(alignPanel, threshold, false, oldCs);
-         sp.cs = oldCs;
-         Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
-       }
-
-       sliderFrame.setContentPane(sp);
-       if(x!=0 && y!=0)
-               sliderFrame.setLocation(x,y);
-
-     }
-     else
-       threshold = 0;
-
-
-     if (oldCs instanceof ResidueColourScheme)
-     {
-       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
-       rcs.setThreshold(threshold);
-     }
-     else if (oldCs instanceof ScoreColourScheme)
-     {
-       ScoreColourScheme scs = (ScoreColourScheme) oldCs;
-       scs.setThreshold(threshold);
-     }
-
-     alignPanel.seqPanel.seqCanvas.paintFlag = true;
-     alignPanel.repaint();
-
-  }
-
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-   if(abovePIDThreshold.isSelected())
-    abovePIDThreshold.setSelected(false);
-
-   viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-   addConservationOrPIDColour();
-  }
-
-  JInternalFrame sliderFrame;
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
-  {
-      if(conservationMenuItem.isSelected())
-        conservationMenuItem.setSelected(false);
-
-      addConservationOrPIDColour();
-  }
-
-
-
-  public void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
-  }
-
-  public void PIDColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new PIDColourScheme() );
-    alignPanel.setColourScheme( );
-  }
-
-
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
-    alignPanel.setColourScheme();
-  }
-*/
-//////////////////////////////////////
-  protected void groupAnnotation_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  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 copyGroup_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
-
-    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) );
-     }
-     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()];
-
-     for (int i=0; i < sg.sequences.size(); i++)
-       s[i] = new Sequence( sg.getSequenceAt(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);
-
-
-     for (int i=0; i < sg.sequences.size(); i++)
-       ap.av.alignment.deleteSequence(sg.getSequenceAt(i));
-
-
-     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
-     ap.RefreshPanels();
-
-
-  }
-
-  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));
-
-    ap.av.alignment.deleteGroup(sg);
-    ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
-    ap.seqPanel.parent.RefreshPanels();
-
-  }
-
-  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();
-
-     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() );
-
-  }
-
-  SequenceGroup getGroup()
-  {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
-
-    // this method won't add a new group if it already exists
-    ap.av.alignment.addGroup(sg);
-    return sg;
-  }
-
-  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);
-
-    if(s!=null)
-    {
-      sequence.setName(s);
-      ap.RefreshPanels();
-    }
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import MCview.*;
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PopupMenu
+    extends JPopupMenu
+{
+  JMenu groupMenu = new JMenu();
+  JMenuItem groupName = new JMenuItem();
+  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem hydrophobicityColour = new
+      JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+  protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  AlignmentPanel ap;
+  JMenu sequenceMenu = new JMenu();
+  JMenuItem sequenceName = new JMenuItem();
+  Sequence sequence;
+  JMenuItem unGroupMenuItem = new JMenuItem();
+  JMenuItem outline = new JMenuItem();
+  JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+  JMenu colourMenu = new JMenu();
+  JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+  JMenu editMenu = new JMenu();
+  JMenuItem cut = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem upperCase = new JMenuItem();
+  JMenuItem lowerCase = new JMenuItem();
+  JMenuItem toggle = new JMenuItem();
+  JMenu pdbMenu = new JMenu();
+  JMenuItem pdbFromFile = new JMenuItem();
+  JMenuItem enterPDB = new JMenuItem();
+  JMenuItem discoverPDB = new JMenuItem();
+  JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+  JMenu structureMenu = new JMenu();
+  JMenu viewStructureMenu = new JMenu();
+ // JMenu colStructureMenu = new JMenu();
+  JMenuItem editSequence = new JMenuItem();
+ // JMenuItem annotationMenuItem = new JMenuItem();
+
+  /**
+   * Creates a new PopupMenu object.
+   *
+   * @param ap DOCUMENT ME!
+   * @param seq DOCUMENT ME!
+   */
+  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+  {
+    ///////////////////////////////////////////////////////////
+    // If this is activated from the sequence panel, the user may want to
+    // edit or annotate a particular residue. Therefore display the residue menu
+    //
+    // If from the IDPanel, we must display the sequence menu
+    //////////////////////////////////////////////////////////
+    this.ap = ap;
+    sequence = seq;
+
+    ButtonGroup colours = new ButtonGroup();
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(abovePIDColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+
+    for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+    {
+      JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
+                                     i]);
+
+      item.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          outputText_actionPerformed(e);
+        }
+      });
+
+      outputMenu.add(item);
+    }
+
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if (seq != null)
+    {
+      sequenceMenu.setText(sequence.getName());
+
+      JMenuItem menuItem;
+      if (seq.getDatasetSequence().getPDBId() != null
+          && seq.getDatasetSequence().getPDBId().size()>0)
+      {
+        java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+            elements();
+
+        while (e.hasMoreElements())
+        {
+          final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+          menuItem = new JMenuItem();
+          menuItem.setText(pdb.getId());
+          menuItem.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              Vector seqs = new Vector();
+              for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+              {
+                Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
+                if(pdbs==null)
+                  continue;
+
+                for(int p=0; p<pdbs.size(); p++)
+                {
+                  PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
+                  if(p1.getId().equals(pdb.getId()))
+                  {
+                    if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
+                        seqs.addElement(ap.av.alignment.getSequenceAt(i));
+
+                      continue;
+                  }
+                }
+              }
+
+              SequenceI [] seqs2 = new SequenceI[seqs.size()];
+              seqs.toArray(seqs2);
+
+              new AppJmol(pdb, seqs2, null, ap);
+              //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+            }
+          });
+          viewStructureMenu.add(menuItem);
+
+       /*   menuItem = new JMenuItem();
+          menuItem.setText(pdb.getId());
+          menuItem.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              colourByStructure(pdb.getId());
+            }
+          });
+          colStructureMenu.add(menuItem);*/
+        }
+      }
+      else
+      {
+        structureMenu.remove(viewStructureMenu);
+       // structureMenu.remove(colStructureMenu);
+      }
+
+      menuItem = new JMenuItem("Hide Sequences");
+      menuItem.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          hideSequences(false);
+        }
+      });
+      add(menuItem);
+
+      if (ap.av.getSelectionGroup() != null
+          && ap.av.getSelectionGroup().getSize() > 1)
+      {
+        menuItem = new JMenuItem("Represent Group with " + seq.getName());
+        menuItem.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            hideSequences(true);
+          }
+        });
+        sequenceMenu.add(menuItem);
+      }
+
+      if (ap.av.hasHiddenRows)
+      {
+        final int index = ap.av.alignment.findIndex(seq);
+
+        if (ap.av.adjustForHiddenSeqs(index) -
+            ap.av.adjustForHiddenSeqs(index - 1) > 1)
+        {
+          menuItem = new JMenuItem("Reveal Sequences");
+          menuItem.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              ap.av.showSequence(index);
+              if (ap.overviewPanel != null)
+              {
+                ap.overviewPanel.updateOverviewImage();
+              }
+            }
+          });
+          add(menuItem);
+        }
+
+        menuItem = new JMenuItem("Reveal All");
+        menuItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            ap.av.showAllHiddenSeqs();
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+
+        add(menuItem);
+      }
+
+    }
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      groupName.setText(sg.getName());
+
+      if (sg.cs instanceof ZappoColourScheme)
+      {
+        zappoColour.setSelected(true);
+      }
+      else if (sg.cs instanceof TaylorColourScheme)
+      {
+        taylorColour.setSelected(true);
+      }
+      else if (sg.cs instanceof PIDColourScheme)
+      {
+        PIDColour.setSelected(true);
+      }
+      else if (sg.cs instanceof Blosum62ColourScheme)
+      {
+        BLOSUM62Colour.setSelected(true);
+      }
+      else if (sg.cs instanceof UserColourScheme)
+      {
+        userDefinedColour.setSelected(true);
+      }
+      else if (sg.cs instanceof HydrophobicColourScheme)
+      {
+        hydrophobicityColour.setSelected(true);
+      }
+      else if (sg.cs instanceof HelixColourScheme)
+      {
+        helixColour.setSelected(true);
+      }
+      else if (sg.cs instanceof StrandColourScheme)
+      {
+        strandColour.setSelected(true);
+      }
+      else if (sg.cs instanceof TurnColourScheme)
+      {
+        turnColour.setSelected(true);
+      }
+      else if (sg.cs instanceof BuriedColourScheme)
+      {
+        buriedColour.setSelected(true);
+      }
+      else if (sg.cs instanceof ClustalxColourScheme)
+      {
+        clustalColour.setSelected(true);
+      }
+      else
+      {
+        noColourmenuItem.setSelected(true);
+      }
+
+      if (sg.cs != null && sg.cs.conservationApplied())
+      {
+        conservationMenuItem.setSelected(true);
+      }
+
+      showText.setSelected(sg.getDisplayText());
+      showColourText.setSelected(sg.getColourText());
+      showBoxes.setSelected(sg.getDisplayBoxes());
+    }
+    else
+    {
+      groupMenu.setVisible(false);
+      editMenu.setVisible(false);
+    }
+
+    if (!ap.av.alignment.getGroups().contains(sg))
+    {
+      unGroupMenuItem.setVisible(false);
+    }
+
+    if (seq == null)
+    {
+      sequenceMenu.setVisible(false);
+      structureMenu.setVisible(false);
+    }
+
+    if (links != null && links.size() > 0)
+    {
+      JMenu linkMenu = new JMenu("Link");
+      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);
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    groupMenu.setText("Group");
+    groupMenu.setText("Selection");
+    groupName.setText("Name");
+    groupName.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        groupName_actionPerformed();
+      }
+    });
+    sequenceMenu.setText("Sequence");
+    sequenceName.setText("Edit Name/Description");
+    sequenceName.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceName_actionPerformed();
+      }
+    });
+    PIDColour.setFocusPainted(false);
+    unGroupMenuItem.setText("Remove Group");
+    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        unGroupMenuItem_actionPerformed();
+      }
+    });
+
+    outline.setText("Border colour");
+    outline.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        outline_actionPerformed();
+      }
+    });
+    nucleotideMenuItem.setText("Nucleotide");
+    nucleotideMenuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideMenuItem_actionPerformed();
+      }
+    });
+    colourMenu.setText("Group Colour");
+    showBoxes.setText("Boxes");
+    showBoxes.setState(true);
+    showBoxes.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showBoxes_actionPerformed();
+      }
+    });
+    showText.setText("Text");
+    showText.setState(true);
+    showText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showText_actionPerformed();
+      }
+    });
+    showColourText.setText("Colour Text");
+    showColourText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showColourText_actionPerformed();
+      }
+    });
+    editMenu.setText("Edit");
+    cut.setText("Cut");
+    cut.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed();
+      }
+    });
+    upperCase.setText("To Upper Case");
+    upperCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    copy.setText("Copy");
+    copy.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed();
+      }
+    });
+    lowerCase.setText("To Lower Case");
+    lowerCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    toggle.setText("Toggle Case");
+    toggle.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    pdbMenu.setText("Associate Structure with Sequence");
+    pdbFromFile.setText("From File");
+    pdbFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pdbFromFile_actionPerformed();
+      }
+    });
+    enterPDB.setText("Enter PDB Id");
+    enterPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        enterPDB_actionPerformed();
+      }
+    });
+    discoverPDB.setText("Discover PDB ids");
+    discoverPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        discoverPDB_actionPerformed();
+      }
+    });
+    outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed();
+      }
+    });
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed();
+      }
+    });
+    jMenu1.setText("Group");
+    structureMenu.setText("Structure");
+    viewStructureMenu.setText("View Structure");
+  //  colStructureMenu.setText("Colour By Structure");
+    editSequence.setText("Edit Sequence...");
+    editSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        editSequence_actionPerformed(actionEvent);
+      }
+    });
+   /* annotationMenuItem.setText("By Annotation");
+    annotationMenuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        annotationMenuItem_actionPerformed(actionEvent);
+      }
+    });*/
+
+    add(groupMenu);
+
+    add(sequenceMenu);
+    this.add(structureMenu);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputMenu);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(jMenu1);
+    sequenceMenu.add(sequenceName);
+    colourMenu.add(textColour);
+    colourMenu.add(noColourmenuItem);
+    colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
+    colourMenu.add(zappoColour);
+    colourMenu.add(taylorColour);
+    colourMenu.add(hydrophobicityColour);
+    colourMenu.add(helixColour);
+    colourMenu.add(strandColour);
+    colourMenu.add(turnColour);
+    colourMenu.add(buriedColour);
+    colourMenu.add(nucleotideMenuItem);
+    colourMenu.add(userDefinedColour);
+
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        JMenuItem item = new JMenuItem(userColours.
+                                       nextElement().toString());
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.add(item);
+      }
+    }
+
+    colourMenu.addSeparator();
+    colourMenu.add(abovePIDColour);
+    colourMenu.add(conservationMenuItem);
+    //colourMenu.add(annotationMenuItem);
+    editMenu.add(copy);
+    editMenu.add(cut);
+    editMenu.add(editSequence);
+    editMenu.add(upperCase);
+    editMenu.add(lowerCase);
+    editMenu.add(toggle);
+    pdbMenu.add(pdbFromFile);
+    pdbMenu.add(enterPDB);
+    pdbMenu.add(discoverPDB);
+    jMenu1.add(groupName);
+    jMenu1.add(unGroupMenuItem);
+    jMenu1.add(colourMenu);
+    jMenu1.add(showBoxes);
+    jMenu1.add(showText);
+    jMenu1.add(showColourText);
+    jMenu1.add(outline);
+    structureMenu.add(pdbMenu);
+    structureMenu.add(viewStructureMenu);
+   // structureMenu.add(colStructureMenu);
+    noColourmenuItem.setText("None");
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed();
+      }
+    });
+
+    clustalColour.setText("Clustalx colours");
+    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clustalColour_actionPerformed();
+      }
+    });
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zappoColour_actionPerformed();
+      }
+    });
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        taylorColour_actionPerformed();
+      }
+    });
+    hydrophobicityColour.setText("Hydrophobicity");
+    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hydrophobicityColour_actionPerformed();
+      }
+    });
+    helixColour.setText("Helix propensity");
+    helixColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        helixColour_actionPerformed();
+      }
+    });
+    strandColour.setText("Strand propensity");
+    strandColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        strandColour_actionPerformed();
+      }
+    });
+    turnColour.setText("Turn propensity");
+    turnColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        turnColour_actionPerformed();
+      }
+    });
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        buriedColour_actionPerformed();
+      }
+    });
+    abovePIDColour.setText("Above % Identity");
+    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDColour_actionPerformed();
+      }
+    });
+    userDefinedColour.setText("User Defined...");
+    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        userDefinedColour_actionPerformed(e);
+      }
+    });
+    PIDColour.setText("Percentage Identity");
+    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PIDColour_actionPerformed();
+      }
+    });
+    BLOSUM62Colour.setText("BLOSUM62");
+    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        BLOSUM62Colour_actionPerformed();
+      }
+    });
+    conservationMenuItem.setText("Conservation");
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed();
+      }
+    });
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  void refresh()
+  {
+    ap.paintAlignment(true);
+
+    PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void clustalColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
+                                     ap.av.alignment.getWidth());
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void zappoColour_actionPerformed()
+  {
+    getGroup().cs = new ZappoColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void taylorColour_actionPerformed()
+  {
+    getGroup().cs = new TaylorColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void hydrophobicityColour_actionPerformed()
+  {
+    getGroup().cs = new HydrophobicColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void helixColour_actionPerformed()
+  {
+    getGroup().cs = new HelixColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void strandColour_actionPerformed()
+  {
+    getGroup().cs = new StrandColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void turnColour_actionPerformed()
+  {
+    getGroup().cs = new TurnColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void buriedColour_actionPerformed()
+  {
+    getGroup().cs = new BuriedColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void nucleotideMenuItem_actionPerformed()
+  {
+    getGroup().cs = new NucleotideColourScheme();
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void abovePIDColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs == null)
+    {
+      return;
+    }
+
+    if (abovePIDColour.isSelected())
+    {
+      sg.cs.setConsensus(AAFrequency.calculate(
+          sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+          sg.getEndRes() + 1));
+
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
+
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+
+      SliderPanel.showPIDSlider();
+    }
+    else // remove PIDColouring
+    {
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+    }
+
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = getGroup();
+
+    if (e.getActionCommand().equals("User Defined..."))
+    {
+      new UserDefinedColours(ap, sg);
+    }
+    else
+    {
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+          getUserColourSchemes().get(e.getActionCommand());
+
+      sg.cs = udc;
+    }
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void PIDColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    sg.cs = new PIDColourScheme();
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences),
+                                             sg.getStartRes(),
+                                             sg.getEndRes() + 1));
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void BLOSUM62Colour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+
+    sg.cs = new Blosum62ColourScheme();
+
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences),
+                                             sg.getStartRes(),
+                                             sg.getEndRes() + 1));
+
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void noColourmenuItem_actionPerformed()
+  {
+    getGroup().cs = null;
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void conservationMenuItem_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs == null)
+    {
+      return;
+    }
+
+    if (conservationMenuItem.isSelected())
+    {
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3,
+                                        sg.getSequences(ap.av.
+          hiddenRepSequences),
+                                        sg.getStartRes(),
+                                        sg.getEndRes() + 1);
+
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
+
+      sg.cs.setConservation(c);
+
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+      SliderPanel.showConservationSlider();
+    }
+    else // remove ConservationColouring
+    {
+      sg.cs.setConservation(null);
+    }
+
+    refresh();
+  }
+
+  public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
+  {
+    SequenceGroup sg = getGroup();
+    if (sg == null)
+    {
+      return;
+    }
+
+    AnnotationColourGradient acg = new AnnotationColourGradient(
+        sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
+
+    acg.predefinedColours = true;
+    sg.cs = acg;
+
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void groupName_actionPerformed()
+  {
+
+    SequenceGroup sg = getGroup();
+    EditNameDialog dialog = new EditNameDialog(sg.getName(),
+                                               sg.getDescription(),
+                                               "       Group Name ",
+                                               "Group Description ",
+                                               "Edit Group Name/Description");
+
+    if (!dialog.accept)
+    {
+      return;
+    }
+
+    sg.setName(dialog.getName());
+    sg.setDescription(dialog.getDescription());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  SequenceGroup getGroup()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    // this method won't add a new group if it already exists
+    if (sg != null)
+    {
+      ap.av.alignment.addGroup(sg);
+    }
+
+    return sg;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  void sequenceName_actionPerformed()
+  {
+    EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+                                               sequence.getDescription(),
+                                               "       Sequence Name ",
+                                               "Sequence Description ",
+                                               "Edit Sequence Name/Description");
+
+    if (!dialog.accept)
+    {
+      return;
+    }
+
+    if (dialog.getName() != null)
+    {
+      if (dialog.getName().indexOf(" ") > -1)
+      {
+        JOptionPane.showMessageDialog(ap,
+                                      "Spaces have been converted to \"_\"",
+                                      "No spaces allowed in Sequence Name",
+                                      JOptionPane.WARNING_MESSAGE);
+      }
+
+      sequence.setName(dialog.getName().replace(' ', '_'));
+      ap.paintAlignment(false);
+    }
+
+    sequence.setDescription(dialog.getDescription());
+
+    ap.av.firePropertyChange("alignment", null,
+                             ap.av.getAlignment().getSequences());
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  void unGroupMenuItem_actionPerformed()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void outline_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+                                         Color.BLUE);
+
+    if (col != null)
+    {
+      sg.setOutlineColour(col);
+    }
+
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showBoxes_actionPerformed()
+  {
+    getGroup().setDisplayBoxes(showBoxes.isSelected());
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showText_actionPerformed()
+  {
+    getGroup().setDisplayText(showText.isSelected());
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showColourText_actionPerformed()
+  {
+    getGroup().setColourText(showColourText.isSelected());
+    refresh();
+  }
+
+  public void showLink(String url)
+  {
+    try
+    {
+      jalview.util.BrowserLauncher.openURL(url);
+    }
+    catch (Exception ex)
+    {
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "Unixers: Couldn't find default web browser."
+                                            +
+          "\nAdd the full path to your browser in Preferences.",
+                                            "Web browser not found",
+                                            JOptionPane.WARNING_MESSAGE);
+
+      ex.printStackTrace();
+    }
+  }
+
+  void hideSequences(boolean representGroup)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null || sg.getSize() < 1)
+    {
+      ap.av.hideSequence(new SequenceI[]
+                         {sequence});
+      return;
+    }
+
+    ap.av.setSelectionGroup(null);
+
+    if (representGroup)
+    {
+      ap.av.hideRepSequences(sequence, sg);
+
+      return;
+    }
+
+    int gsize = sg.getSize();
+    SequenceI[] hseqs;
+
+    hseqs = new SequenceI[gsize];
+
+    int index = 0;
+    for (int i = 0; i < gsize; i++)
+    {
+      hseqs[index++] = sg.getSequenceAt(i);
+    }
+
+    ap.av.hideSequence(hseqs);
+  }
+
+  public void copy_actionPerformed()
+  {
+    ap.alignFrame.copy_actionPerformed(null);
+  }
+
+  public void cut_actionPerformed()
+  {
+    ap.alignFrame.cut_actionPerformed(null);
+  }
+
+  void changeCase(ActionEvent e)
+  {
+    Object source = e.getSource();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+          sg.getStartRes(), sg.getEndRes() + 1);
+
+      String description;
+      int caseChange;
+
+      if (source == toggle)
+      {
+        description = "Toggle Case";
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;
+      }
+      else if (source == upperCase)
+      {
+        description = "To Upper Case";
+        caseChange = ChangeCaseCommand.TO_UPPER;
+      }
+      else
+      {
+        description = "To Lower Case";
+        caseChange = ChangeCaseCommand.TO_LOWER;
+      }
+
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
+          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+          startEnd, caseChange
+          );
+
+      ap.alignFrame.addHistoryItem(caseCommand);
+
+      ap.av.firePropertyChange("alignment", null,
+                               ap.av.getAlignment().getSequences());
+
+    }
+  }
+
+  public void outputText_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
+
+    String[] omitHidden = null;
+
+    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
+    omitHidden = ap.av.getViewAsString(true);
+    Alignment oal = new Alignment(ap.av.getSequenceSelection());
+    AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+    for (int i=0; i<nala.length; i++)
+    {
+      AlignmentAnnotation na =nala[i];
+      oal.addAnnotation(na);
+    }
+    cap.setText(new FormatAdapter().formatSequences(
+            e.getActionCommand(),
+            oal,
+            omitHidden, csel, sg));
+    oal=null;
+  }
+
+  public void pdbFromFile_actionPerformed()
+  {
+    jalview.io.JalviewFileChooser chooser
+        = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
+                                            getProperty(
+                                                "LAST_DIRECTORY"));
+    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setDialogTitle("Select a PDB file");
+    chooser.setToolTipText("Load a PDB file");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    {
+      PDBEntry entry = new PDBEntry();
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      try
+      {
+        MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+            jalview.io.AppletFormatAdapter.FILE);
+
+        if (pdbfile.id == null)
+        {
+          String reply = JOptionPane.showInternalInputDialog(
+              Desktop.desktop,
+              "Couldn't find a PDB id in the file supplied."
+              + "Please enter an Id to identify this structure.",
+              "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+          if (reply == null)
+          {
+            return;
+          }
+
+          entry.setId(reply);
+        }
+        else
+        {
+          entry.setId(pdbfile.id);
+        }
+      }
+      catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+
+      entry.setFile(choice);
+      sequence.getDatasetSequence().addPDBId(entry);
+    }
+
+  }
+
+  public void enterPDB_actionPerformed()
+  {
+    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+    if (id != null && id.length() > 0)
+    {
+      PDBEntry entry = new PDBEntry();
+      entry.setId(id.toUpperCase());
+      sequence.getDatasetSequence()
+          .addPDBId(entry);
+    }
+  }
+
+  public void discoverPDB_actionPerformed()
+  {
+    SequenceI[] sequences =
+         ap.av.selectionGroup == null ?
+           new Sequence[]{sequence}
+         : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
+
+    new jalview.ws.DBRefFetcher(sequences,
+        ap.alignFrame).fetchDBRefs(false);
+  }
+
+  public void sequenceFeature_actionPerformed()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null)
+    {
+      return;
+    }
+
+    int gSize = sg.getSize();
+    SequenceI[] seqs = new SequenceI[gSize];
+    SequenceFeature[] features = new SequenceFeature[gSize];
+
+    for (int i = 0; i < gSize; i++)
+    {
+      seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+      int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+      int end = sg.findEndRes(sg.getSequenceAt(i));
+      features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
+    }
+
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .amendFeatures(seqs, features, true, ap))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
+
+  public void textColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg != null)
+    {
+      new TextColourChooser().chooseColour(ap, sg);
+    }
+  }
+
+  public void colourByStructure(String pdbid)
+  {
+    Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+        .colourSequenceFromStructure(sequence, pdbid);
+
+    AlignmentAnnotation an = new AlignmentAnnotation(
+      "Structure", "Coloured by "+pdbid, anots);
+
+    ap.av.alignment.addAnnotation(an);
+    an.createSequenceMapping(sequence, 0, true);
+    //an.adjustForAlignment();
+    ap.av.alignment.setAnnotationIndex(an,0);
+
+    ap.adjustAnnotationHeight();
+
+    sequence.addAlignmentAnnotation(an);
+
+    }
+
+  public void editSequence_actionPerformed(ActionEvent actionEvent)
+  {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+
+      if(sg!=null)
+      {
+        if (sequence == null)
+          sequence = (Sequence) sg.getSequenceAt(0);
+
+        EditNameDialog dialog = new EditNameDialog(
+            sequence.getSequenceAsString(
+                sg.getStartRes(),
+                sg.getEndRes() + 1),
+            null,
+            "Edit Sequence ",
+            null,
+            "Edit Sequence");
+
+        if (dialog.accept)
+        {
+          EditCommand editCommand = new EditCommand(
+              "Edit Sequences", EditCommand.REPLACE,
+              dialog.getName().replace(' ', ap.av.getGapCharacter()),
+              sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+              sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
+              );
+
+          ap.alignFrame.addHistoryItem(editCommand);
+
+          ap.av.firePropertyChange("alignment", null,
+                                   ap.av.getAlignment().getSequences());
+        }
+      }
+  }
+
+
+}