X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f1a38f5475b4193e0f2077803b049d566f193a89;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=d85fabcc1a5978df2d537d49a44c30616c64d9a5;hpb=b618755c67d798ace34ebd6d0f384e913e8574c9;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index d85fabc..f1a38f5 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,22 +1,52 @@
+/*
+ * 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 jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
+import java.util.*;
+
 import java.awt.*;
-import javax.swing.*;
 import java.awt.event.*;
-import jalview.io.*;
+import javax.swing.*;
+
 import MCview.*;
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
 
-public class PopupMenu extends JPopupMenu
+/**
+ * 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 hydrophobicityColour = new
+      JRadioButtonMenuItem();
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
@@ -27,22 +57,39 @@ public class PopupMenu extends JPopupMenu
   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();
-
-  public PopupMenu(AlignmentPanel ap, Sequence seq)
+  JMenu editMenu = new JMenu();
+  JMenuItem cut = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem upperCase = new JMenuItem();
+  JMenuItem lowerCase = new JMenuItem();
+  JMenuItem toggle = new JMenuItem();
+  JMenu pdbMenu = new JMenu();
+  JMenuItem pdbFromFile = new JMenuItem();
+  JMenuItem enterPDB = new JMenuItem();
+  JMenuItem discoverPDB = new JMenuItem();
+  JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+
+  /**
+   * Creates a new PopupMenu object.
+   *
+   * @param ap DOCUMENT ME!
+   * @param seq DOCUMENT ME!
+   */
+  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -50,7 +97,6 @@ public class PopupMenu extends JPopupMenu
     //
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
-
     this.ap = ap;
     sequence = seq;
 
@@ -69,76 +115,278 @@ public class PopupMenu extends JPopupMenu
     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();    }
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if (seq != null)
+    {
+      sequenceMenu.setText(sequence.getName());
+
+      JMenuItem menuItem;
+      if (seq.getDatasetSequence().getPDBId() != null)
+      {
+        java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+            elements();
+
+        while (e.hasMoreElements())
+        {
+          final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+          menuItem = new JMenuItem();
+          menuItem.setText("View PDB entry: " + pdb.getId());
+          menuItem.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
+            }
+          });
+          sequenceMenu.add(menuItem);
+        }
+      }
+
+      menuItem = new JMenuItem("Hide Sequences");
+      menuItem.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          hideSequences(false);
+        }
+      });
+      add(menuItem);
+
+      if (ap.av.getSelectionGroup() != null
+          && ap.av.getSelectionGroup().getSize() > 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)
+
+    if (sg != null)
     {
       groupName.setText(sg.getName());
-      if(sg.cs instanceof ZappoColourScheme)
+
+      if (sg.cs instanceof ZappoColourScheme)
+      {
         zappoColour.setSelected(true);
-      else if(sg.cs instanceof TaylorColourScheme)
+      }
+      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)
+      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))
+    if (!ap.av.alignment.getGroups().contains(sg))
+    {
       unGroupMenuItem.setVisible(false);
-    else
-      groupMenu.insertSeparator(3);
+    }
 
-    if(seq==null)
-       sequenceMenu.setVisible(false);
+    if (seq == null)
+    {
+      sequenceMenu.setVisible(false);
+      pdbMenu.setVisible(false);
+    }
 
+    if (links != null && links.size() > 0)
+    {
+      JMenu linkMenu = new JMenu("Link");
+      JMenuItem item;
+      for (int i = 0; i < links.size(); i++)
+      {
+        String link = links.elementAt(i).toString();
+        final String label = link.substring(0, link.indexOf("|"));
+        item = new JMenuItem(label);
+        final String url;
+
+        if (link.indexOf("$SEQUENCE_ID$") > -1)
+        {
+          String id = seq.getName();
+          if (id.indexOf("|") > -1)
+          {
+            id = id.substring(id.lastIndexOf("|") + 1);
+          }
+
+          url = link.substring(link.indexOf("|") + 1,
+                               link.indexOf("$SEQUENCE_ID$"))
+              + id +
+              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+        }
+        else
+        {
+          url = link.substring(link.lastIndexOf("|") + 1);
+        }
+
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            showLink(url);
+          }
+        });
+
+        linkMenu.add(item);
+      }
+      if (sequence != null)
+      {
+        sequenceMenu.add(linkMenu);
+      }
+      else
+      {
+        add(linkMenu);
+      }
+    }
   }
-  private void jbInit() throws Exception
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
   {
     groupMenu.setText("Group");
-    groupMenu.setText("Define");
+    groupMenu.setText("Selection");
     groupName.setText("Name");
     groupName.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        groupName_actionPerformed(e);
+        groupName_actionPerformed();
       }
     });
     sequenceMenu.setText("Sequence");
-    sequenceName.setText("Edit name");
+    sequenceName.setText("Edit Name/Description");
     sequenceName.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        sequenceName_actionPerformed(e);
+        sequenceName_actionPerformed();
       }
     });
     PIDColour.setFocusPainted(false);
@@ -147,23 +395,16 @@ public class PopupMenu extends JPopupMenu
     {
       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);
+        unGroupMenuItem_actionPerformed();
       }
     });
+
     outline.setText("Border colour");
     outline.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        outline_actionPerformed(e);
+        outline_actionPerformed();
       }
     });
     nucleotideMenuItem.setText("Nucleotide");
@@ -171,7 +412,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        nucleotideMenuItem_actionPerformed(e);
+        nucleotideMenuItem_actionPerformed();
       }
     });
     colourMenu.setText("Group Colour");
@@ -181,7 +422,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        showBoxes_actionPerformed(e);
+        showBoxes_actionPerformed();
       }
     });
     showText.setText("Text");
@@ -190,7 +431,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        showText_actionPerformed(e);
+        showText_actionPerformed();
       }
     });
     showColourText.setText("Colour Text");
@@ -198,23 +439,103 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        showColourText_actionPerformed(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");
     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);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputMenu);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(jMenu1);
     sequenceMenu.add(sequenceName);
-    sequenceMenu.add(pdbMenuItem);
+    sequenceMenu.add(pdbMenu);
+    colourMenu.add(textColour);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -228,15 +549,51 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
     colourMenu.add(userDefinedColour);
+
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        JMenuItem item = new JMenuItem(userColours.
+                                       nextElement().toString());
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.add(item);
+      }
+    }
+
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
+    editMenu.add(copy);
+    editMenu.add(cut);
+    editMenu.add(upperCase);
+    editMenu.add(lowerCase);
+    editMenu.add(toggle);
+    pdbMenu.add(pdbFromFile);
+    pdbMenu.add(enterPDB);
+    pdbMenu.add(discoverPDB);
+    jMenu1.add(groupName);
+    jMenu1.add(unGroupMenuItem);
+    jMenu1.add(colourMenu);
+    jMenu1.add(showBoxes);
+    jMenu1.add(showText);
+    jMenu1.add(showColourText);
+    jMenu1.add(outline);
     noColourmenuItem.setText("None");
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        noColourmenuItem_actionPerformed(e);
+        noColourmenuItem_actionPerformed();
       }
     });
 
@@ -245,7 +602,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        clustalColour_actionPerformed(e);
+        clustalColour_actionPerformed();
       }
     });
     zappoColour.setText("Zappo");
@@ -253,7 +610,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        zappoColour_actionPerformed(e);
+        zappoColour_actionPerformed();
       }
     });
     taylorColour.setText("Taylor");
@@ -261,7 +618,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        taylorColour_actionPerformed(e);
+        taylorColour_actionPerformed();
       }
     });
     hydrophobicityColour.setText("Hydrophobicity");
@@ -269,7 +626,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        hydrophobicityColour_actionPerformed(e);
+        hydrophobicityColour_actionPerformed();
       }
     });
     helixColour.setText("Helix propensity");
@@ -277,7 +634,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        helixColour_actionPerformed(e);
+        helixColour_actionPerformed();
       }
     });
     strandColour.setText("Strand propensity");
@@ -285,7 +642,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        strandColour_actionPerformed(e);
+        strandColour_actionPerformed();
       }
     });
     turnColour.setText("Turn propensity");
@@ -293,7 +650,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        turnColour_actionPerformed(e);
+        turnColour_actionPerformed();
       }
     });
     buriedColour.setText("Buried Index");
@@ -301,7 +658,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        buriedColour_actionPerformed(e);
+        buriedColour_actionPerformed();
       }
     });
     abovePIDColour.setText("Above % Identity");
@@ -309,10 +666,10 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDColour_actionPerformed(e);
+        abovePIDColour_actionPerformed();
       }
     });
-    userDefinedColour.setText("User Defined");
+    userDefinedColour.setText("User Defined...");
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -325,7 +682,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        PIDColour_actionPerformed(e);
+        PIDColour_actionPerformed();
       }
     });
     BLOSUM62Colour.setText("BLOSUM62");
@@ -333,303 +690,689 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        BLOSUM62Colour_actionPerformed(e);
+        BLOSUM62Colour_actionPerformed();
       }
     });
     conservationMenuItem.setText("Conservation");
-   conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-   {
-     public void actionPerformed(ActionEvent e)
-     {
-       conservationMenuItem_actionPerformed(e);
-     }
-   });
-
-
-
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed();
+      }
+    });
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   void refresh()
   {
-    SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
-    if( superG !=null)
-      superG.setSuperGroupProperties( sg );
+    if (ap.overviewPanel != null)
+    {
+      ap.overviewPanel.updateOverviewImage();
+    }
 
-    ap.seqPanel.repaint();
+    PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
   }
 
-  protected void clustalColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
+                                     ap.av.alignment.getWidth());
     refresh();
   }
 
-  protected void zappoColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void zappoColour_actionPerformed()
   {
     getGroup().cs = new ZappoColourScheme();
     refresh();
   }
 
-  protected void taylorColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void taylorColour_actionPerformed()
   {
     getGroup().cs = new TaylorColourScheme();
     refresh();
   }
 
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void hydrophobicityColour_actionPerformed()
   {
     getGroup().cs = new HydrophobicColourScheme();
     refresh();
   }
 
-  protected void helixColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void helixColour_actionPerformed()
   {
     getGroup().cs = new HelixColourScheme();
     refresh();
   }
 
-  protected void strandColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void strandColour_actionPerformed()
   {
     getGroup().cs = new StrandColourScheme();
     refresh();
   }
 
-  protected void turnColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void turnColour_actionPerformed()
   {
     getGroup().cs = new TurnColourScheme();
     refresh();
   }
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void buriedColour_actionPerformed()
   {
     getGroup().cs = new BuriedColourScheme();
     refresh();
   }
 
-  public void nucleotideMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void nucleotideMenuItem_actionPerformed()
   {
     getGroup().cs = new NucleotideColourScheme();
     refresh();
   }
 
-
-
-  protected void abovePIDColour_actionPerformed(ActionEvent e)
+  /**
+   * 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.sequences, 0,
-                                               ap.av.alignment.getWidth()));
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
-      if (sg.cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
-      else if (sg.cs instanceof ScoreColourScheme)
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+      sg.cs.setConsensus(AAFrequency.calculate(
+          sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+          sg.getEndRes() + 1));
 
-      SliderPanel.showPIDSlider();
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
 
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
+      SliderPanel.showPIDSlider();
     }
     else // remove PIDColouring
     {
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-      rcs.setThreshold(0);
-      sg.cs = rcs;
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
 
     refresh();
-
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    new UserDefinedColours( ap, getGroup());
+    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();
   }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void PIDColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences),
+                                             sg.getStartRes(),
+                                             sg.getEndRes() + 1));
     refresh();
   }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void BLOSUM62Colour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences),
+                                             sg.getStartRes(),
+                                             sg.getEndRes() + 1));
 
     refresh();
   }
 
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void noColourmenuItem_actionPerformed()
   {
     getGroup().cs = null;
     refresh();
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void conservationMenuItem_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-
-    if(conservationMenuItem.isSelected())
+    if (sg.cs == null)
     {
+      return;
+    }
 
-        Conservation c = new Conservation("Group",
-                                          ResidueProperties.propHash, 3,
-                                          sg.sequences, 0,
-                                          ap.av.alignment.getWidth());
-
-        c.calculate();
-        c.verdict(false, ap.av.ConsPercGaps);
-        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+    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 = ccs;
+      sg.cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
-        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-        sg.cs = ccs.cs;
+      sg.cs.setConservation(null);
     }
 
-     refresh();
+    refresh();
   }
 
-
-  protected void groupName_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void groupName_actionPerformed()
   {
+
     SequenceGroup sg = getGroup();
-    String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
-    if(reply==null)
+    EditNameDialog dialog = new EditNameDialog(sg.getName(),
+                                               sg.getDescription(),
+                                               "       Group Name ",
+                                               "Group Description ",
+                                               "Edit Group Name/Description");
+
+    if (!dialog.accept)
+    {
       return;
+    }
 
-    sg.setName(reply);
-    groupName.setText(reply);
+    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);
+    }
 
-  protected void analyze_actionPerformed(ActionEvent e)
+    return sg;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  void sequenceName_actionPerformed()
   {
-     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();
+    EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+                                               sequence.getDescription(),
+                                               "       Sequence Name ",
+                                               "Sequence Description ",
+                                               "Edit Sequence Name/Description");
 
-     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");
-     }
+    if (!dialog.accept)
+    {
+      return;
+    }
 
-     sb.append("Something amazing will happen soon");
-     cap.setText( sb.toString() );
+    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.repaint();
+    }
+
+    sequence.setDescription(dialog.getDescription());
+
+    ap.av.firePropertyChange("alignment", null,
+                             ap.av.getAlignment().getSequences());
 
   }
 
-  SequenceGroup getGroup()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  void unGroupMenuItem_actionPerformed()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    refresh();
+  }
 
-    // this method won't add a new group if it already exists
-    ap.av.alignment.addGroup(sg);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void outline_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+                                         Color.BLUE);
 
-    return sg;
+    if (col != null)
+    {
+      sg.setOutlineColour(col);
+    }
+
+    refresh();
   }
 
-  void sequenceName_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showBoxes_actionPerformed()
   {
-    String id = sequence.getName();
-    String s = (String)JOptionPane.showInternalInputDialog(
-                ap,
-                "Edit sequence name",
-                "Edit sequence name ("+sequence.getName()+")",
-                JOptionPane.PLAIN_MESSAGE,
-                null,
-                null,
-                id);
+    getGroup().setDisplayBoxes(showBoxes.isSelected());
+    refresh();
+  }
 
-    if(s!=null)
+  /**
+   * 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
     {
-      sequence.setName(s);
-      ap.repaint();
+      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 unGroupMenuItem_actionPerformed(ActionEvent e)
+  void hideSequences(boolean representGroup)
   {
-     SequenceGroup sg = ap.av.getSelectionGroup();
-     ap.av.alignment.deleteGroup(sg);
-     ap.av.setSelectionGroup(null);
-     ap.repaint();
+    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);
   }
 
-  void pdbMenuItem_actionPerformed(ActionEvent e)
+  public void copy_actionPerformed()
   {
-    if(sequence.getPDBId()==null)
-      return;
+    ap.alignFrame.copy_actionPerformed(null);
+  }
 
-    try
+  public void cut_actionPerformed()
+  {
+    ap.alignFrame.cut_actionPerformed(null);
+  }
+
+  void changeCase(ActionEvent e)
+  {
+    Object source = e.getSource();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    Vector regions = new Vector();
+    if (sg != null)
     {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
+      int start = sg.getStartRes();
+      int end = sg.getEndRes() + 1;
 
-      PDBfile pdb = new PDBfile(result);
+      do
+      {
+        if (ap.av.hasHiddenColumns)
+        {
+          if (start == 0)
+          {
+            start = ap.av.colSel.adjustForHiddenColumns(start);
+          }
+
+          end = ap.av.colSel.getHiddenBoundaryRight(start);
+          if (start == end)
+          {
+            end = sg.getEndRes() + 1;
+          }
+          if (end > sg.getEndRes())
+          {
+            end = sg.getEndRes() + 1;
+          }
+        }
+
+        regions.addElement(new int[]
+                           {start, end});
+
+        if (ap.av.hasHiddenColumns)
+        {
+          start = ap.av.colSel.adjustForHiddenColumns(end);
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+        }
+      }
+      while (end < sg.getEndRes());
+
+      int[][] startEnd = new int[regions.size()][2];
+      for (int i = 0; i < regions.size(); i++)
+      {
+        startEnd[i] = (int[]) regions.elementAt(i);
+      }
+
+      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());
 
-      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)
+  }
+
+  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;
+
+    if (ap.av.hasHiddenColumns)
     {
-      ex.printStackTrace();
+      System.out.println("PROMPT USER HERE");
+      omitHidden = ap.av.getViewAsString(true);
     }
+
+    cap.setText(new FormatAdapter().formatSequences(
+        e.getActionCommand(),
+        ap.av.getSelectionAsNewSequence(),
+        omitHidden));
   }
 
-  protected void outline_actionPerformed(ActionEvent e)
+  public void pdbFromFile_actionPerformed()
   {
-    SequenceGroup sg = getGroup();
-    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
-    if(col!=null)
-      sg.setOutlineColour(col);
-    ap.repaint();
+    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 showBoxes_actionPerformed(ActionEvent e)
+  public void enterPDB_actionPerformed()
   {
-    getGroup().setDisplayBoxes(showBoxes.isSelected());
-    refresh();
+    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+    if (id != null && id.length() > 0)
+    {
+      PDBEntry entry = new PDBEntry();
+      entry.setId(id);
+      sequence.getDatasetSequence()
+          .addPDBId(entry);
+    }
   }
 
-  public void showText_actionPerformed(ActionEvent e)
+  public void discoverPDB_actionPerformed()
   {
-    getGroup().setDisplayText(showText.isSelected());
-    refresh();
+    new jalview.io.DBRefFetcher(
+        ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
   }
 
-  public void showColourText_actionPerformed(ActionEvent e)
+  public void sequenceFeature_actionPerformed()
   {
-    getGroup().setColourText(showColourText.isSelected());
-    refresh();
+    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()
+        .createNewFeatures(seqs, features))
+    {
+      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);
+    }
+  }
 }