X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=4b28166e395d450b8cf487c8085a3315a8915d30;hb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;hp=484b8cd93ea6667b69fad2544c17e7d3fc662838;hpb=e588028667ea7c02f015c9ecc2be2f811e3d761b;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 484b8cd..4b28166 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -13,12 +13,13 @@
  * 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
+ * along with this program; if not, write to the Free Softwarechang
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.gui;
 
 import java.beans.*;
+import java.io.*;
 import java.util.*;
 
 import java.awt.*;
@@ -35,18 +36,34 @@ import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.ws.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class AlignFrame
     extends GAlignFrame
 {
+  /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
+
+  /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_HEIGHT = 500;
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
-  public String currentFileFormat = "Jalview";
+
+  /** DOCUMENT ME!! */
+  public String currentFileFormat = null;
   Stack historyList = new Stack();
   Stack redoList = new Stack();
   private int treeCount = 0;
 
+  /**
+   * Creates a new AlignFrame object.
+   *
+   * @param al DOCUMENT ME!
+   */
   public AlignFrame(AlignmentI al)
   {
     viewport = new AlignViewport(al);
@@ -59,23 +76,132 @@ public class AlignFrame
         getPreferredSize());
     alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
 
+    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+    if(sortby.equals("Id"))
+      sortIDMenuItem_actionPerformed(null);
+    else if(sortby.equals("Pairwise Identity"))
+      sortPairwiseMenuItem_actionPerformed(null);
+
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
-    addInternalFrameListener(new InternalFrameAdapter()
+    viewport.addPropertyChangeListener(new PropertyChangeListener()
+    {
+     public void propertyChange(PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
+
+    addServiceListeners();
+  }
+
+  /* Set up intrinsic listeners for dynamically generated GUI bits. */
+  private void addServiceListeners()
+  {
+    final java.beans.PropertyChangeListener thisListener;
+    // Do this once to get current state
+    BuildWebServiceMenu();
+    Desktop.discoverer.addPropertyChangeListener(
+        thisListener = new java.beans.PropertyChangeListener()
+    {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        // System.out.println("Discoverer property change.");
+        if (evt.getPropertyName().equals("services"))
+        {
+          // System.out.println("Rebuilding web service menu");
+          BuildWebServiceMenu();
+        }
+      }
+    });
+    addInternalFrameListener(new javax.swing.event.
+                             InternalFrameAdapter()
+    {
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
+      {
+        // System.out.println("deregistering discoverer listener");
+        Desktop.discoverer.removePropertyChangeListener(thisListener);
+        closeMenuItem_actionPerformed(null);
+      }
+      ;
+    });
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param String DOCUMENT ME!
+   */
+
+  public void parseGroupsFile(String file)
+  {
+    try
     {
-      public void internalFrameActivated(InternalFrameEvent evt)
+      BufferedReader in = new BufferedReader(new FileReader(file));
+      SequenceI seq = null;
+      String line, text, token;
+      UserColourScheme ucs;
+      int index, start, end;
+      StringTokenizer st;
+      SequenceGroup sg;
+      while ( (line = in.readLine()) != null)
       {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() != 6)
+        {
+          System.out.println("Groups file " + file +
+                             " is invalid. Read help file.");
+          System.exit(1);
+        }
+
+        while (st.hasMoreElements())
         {
-          public void run()
+          text = st.nextToken();
+          token = st.nextToken();
+          if (!token.equals("ID_NOT_SPECIFIED"))
           {
-            alignPanel.requestFocus();
+            index = viewport.alignment.findIndex(viewport.alignment.findName(
+                token));
+            st.nextToken();
           }
-        });
+          else
+          {
+            index = Integer.parseInt(st.nextToken());
+          }
+
+          start = Integer.parseInt(st.nextToken());
+          end = Integer.parseInt(st.nextToken());
+          ucs = new UserColourScheme(st.nextToken());
+
+          seq = viewport.alignment.getSequenceAt(index);
+          start = seq.findIndex(start) - 1;
+          end = seq.findIndex(end) - 1;
+
+          sg = new SequenceGroup(text, ucs, true, true, false, start, end);
+          sg.addSequence(seq, true);
+
+          viewport.alignment.addGroup(sg);
+        }
       }
-    });
+
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Error parsing groups file: " + ex);
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
@@ -104,43 +230,62 @@ public class AlignFrame
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                     currentFileFormat);
 
-      if (currentFileFormat.equals("Jalview"))
-      {
-        String shortName = title;
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
 
-        if (shortName.indexOf(java.io.File.separatorChar) > -1)
-        {
-          shortName = shortName.substring(shortName.lastIndexOf(
-              java.io.File.separatorChar) + 1);
-        }
+      saveAlignment(choice, currentFileFormat);
+    }
+  }
 
-        String choice = chooser.getSelectedFile().getPath();
-        Jalview2XML.SaveAlignment(this, choice, shortName);
+  public boolean saveAlignment(String file, String format)
+  {
+    if (format.equalsIgnoreCase("Jalview"))
+    {
+      String shortName = title;
 
-        // USE Jalview2XML to save this file
-        return;
+      if (shortName.indexOf(java.io.File.separatorChar) > -1)
+      {
+        shortName = shortName.substring(shortName.lastIndexOf(
+            java.io.File.separatorChar) + 1);
       }
 
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      Jalview2XML.SaveAlignment(this, file, shortName);
 
-      String output = FormatAdapter.formatSequences(currentFileFormat,
-          viewport.getAlignment().getSequences());
+      // USE Jalview2XML to save this file
+      return true;
+    }
+    else
+    {
+      String output = FormatAdapter.formatSequences(format,
+          viewport.getAlignment().
+          getSequences());
+      if (output == null)
+      {
+        return false;
+      }
 
       try
       {
-        java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
-            FileWriter(
-                choice));
-        out.println(output);
+        java.io.PrintWriter out = new java.io.PrintWriter(
+            new java.io.FileWriter(file));
+
+        out.print(output);
         out.close();
+        return true;
       }
       catch (Exception ex)
       {
+        ex.printStackTrace();
       }
     }
+    return false;
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void outputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -152,21 +297,46 @@ public class AlignFrame
                                               getSequences()));
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     new HTMLOutput(viewport);
   }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
+  public void createImageMap(File file, String image)
   {
-    alignPanel.makePNG();
+    alignPanel.makePNGImageMap(file, image);
   }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createPNG(File f)
   {
-    alignPanel.makeEPS();
+    alignPanel.makePNG(f);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createEPS(File f)
+  {
+    alignPanel.makeEPS(f);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     //Putting in a thread avoids Swing painting problems
@@ -174,10 +344,16 @@ public class AlignFrame
     thread.start();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
     try
     {
+      PaintRefresher.components.remove(viewport.alignment);
       this.setClosed(true);
     }
     catch (Exception ex)
@@ -185,6 +361,9 @@ public class AlignFrame
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   void updateEditMenuBar()
   {
     if (historyList.size() > 0)
@@ -214,28 +393,42 @@ public class AlignFrame
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param hi DOCUMENT ME!
+   */
   public void addHistoryItem(HistoryItem hi)
   {
     historyList.push(hi);
     updateEditMenuBar();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
     HistoryItem hi = (HistoryItem) historyList.pop();
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
     HistoryItem hi = (HistoryItem) redoList.pop();
     restoreHistoryItem(hi);
     updateEditMenuBar();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   // used by undo and redo
@@ -280,13 +473,15 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
     viewport.firePropertyChange("alignment", null,
                                 viewport.getAlignment().getSequences());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param up DOCUMENT ME!
+   */
   public void moveSelectedSequences(boolean up)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -344,6 +539,11 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void copy_actionPerformed(ActionEvent e)
   {
     if (viewport.getSelectionGroup() == null)
@@ -365,7 +565,8 @@ public class AlignFrame
       orderedSeqs.put(index + "", seq);
     }
 
-    int index = 0;
+    int index = 0, startRes, endRes;
+    char ch;
 
     for (int i = 0; i < sg.getSize(); i++)
     {
@@ -385,22 +586,53 @@ public class AlignFrame
           index++;
         }
       }
+      //FIND START RES
+      //Returns residue following index if gap
+      startRes = seq.findPosition(sg.getStartRes());
+
+      //FIND END RES
+      //Need to find the residue preceeding index if gap
+      endRes = 0;
+
+      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
+      {
+        ch = seq.getCharAt(j);
+        if (!jalview.util.Comparison.isGap( (ch)))
+        {
+          endRes++;
+        }
+      }
+
+      if (endRes > 0)
+      {
+        endRes += seq.getStart() - 1;
+      }
 
       buffer.append(seq.getName() + "\t" +
-                    seq.findPosition(sg.getStartRes()) + "\t" +
-                    seq.findPosition(sg.getEndRes()) + "\t" +
-                    sg.getSequenceAt(i).getSequence(sg.getStartRes(),
-          sg.getEndRes() + 1) + "\n");
+                    startRes + "\t" +
+                    endRes + "\t" +
+                    seq.getSequence(sg.getStartRes(),
+                                    sg.getEndRes() + 1) + "\n");
     }
 
     c.setContents(new StringSelection(buffer.toString()), null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
     paste(true);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
@@ -408,6 +640,11 @@ public class AlignFrame
     paste(false);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param newAlignment DOCUMENT ME!
+   */
   void paste(boolean newAlignment)
   {
     try
@@ -464,28 +701,35 @@ public class AlignFrame
       }
       else
       {
-        viewport.firePropertyChange("alignment", null,
-                                    viewport.getAlignment().getSequences());
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       }
     }
     catch (Exception ex)
     {
+        // could be anything being pasted in here
     }
 
-    // could be anything being pasted in here
+
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void cut_actionPerformed(ActionEvent e)
   {
     copy_actionPerformed(null);
     delete_actionPerformed(null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void delete_actionPerformed(ActionEvent e)
   {
     boolean seqsdeleted = false;
@@ -499,6 +743,11 @@ public class AlignFrame
                                    HistoryItem.HIDE));
 
     SequenceGroup sg = viewport.getSelectionGroup();
+    boolean allSequences = false;
+    if (sg.sequences.size() == viewport.alignment.getHeight())
+    {
+      allSequences = true;
+    }
 
     for (int i = 0; i < sg.sequences.size(); i++)
     {
@@ -506,6 +755,13 @@ public class AlignFrame
       int index = viewport.getAlignment().findIndex(seq);
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
+      // If the cut affects all sequences, remove highlighted columns
+      if (allSequences)
+      {
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),
+            sg.getEndRes() + 1);
+      }
+
       if (seq.getSequence().length() < 1)
       {
         seqsdeleted = true;
@@ -526,7 +782,6 @@ public class AlignFrame
                                   viewport.getAlignment().getSequences());
     }
 
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -538,12 +793,13 @@ public class AlignFrame
       {
       }
     }
-
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
@@ -551,6 +807,11 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = new SequenceGroup();
@@ -561,26 +822,38 @@ public class AlignFrame
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    sg.setEndRes(viewport.alignment.getWidth());
+    sg.setEndRes(viewport.alignment.getWidth() - 1);
     viewport.setSelectionGroup(sg);
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    alignPanel.annotationPanel.activeRes=null;
+    alignPanel.annotationPanel.activeRes = null;
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
-    if(sg==null)
+
+    if (sg == null)
     {
       selectAllSequenceMenuItem_actionPerformed(null);
+
       return;
     }
 
@@ -593,6 +866,11 @@ public class AlignFrame
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
@@ -623,10 +901,15 @@ public class AlignFrame
         }
       }
 
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
@@ -656,36 +939,77 @@ public class AlignFrame
         }
       }
 
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                    viewport.alignment, HistoryItem.HIDE));
 
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
     viewport.getAlignment().removeGaps();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
 
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
+
     SequenceI current;
     int jSize;
 
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
+    Vector seqs = null;
+
+    int start = 0;
+    int end = viewport.alignment.getWidth();
+
+    if (viewport.getSelectionGroup() != null
+        && viewport.getSelectionGroup().sequences != null
+        && viewport.getSelectionGroup().sequences.size() > 0)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
+      seqs = viewport.getSelectionGroup().sequences;
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+    {
+      seqs = viewport.alignment.getSequences();
+    }
+
+    for (int i = 0; i < seqs.size(); i++)
+    {
+      current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
 
-      for (int j = 0; j < jSize; j++)
+      int j = start;
+
+      do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
@@ -693,14 +1017,69 @@ public class AlignFrame
           j--;
           jSize--;
         }
+        j++;
       }
+      while (j < end && j < jSize);
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
+ public void alignmentChanged()
+ {
+   viewport.updateConsensus();
+   viewport.updateConservation();
+   resetAllColourSchemes();
+   alignPanel.repaint();
+ }
+
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+            resetClustalX(viewport.alignment.getSequences(),
+                          viewport.alignment.getWidth());
+      }
+
+      cs.setConsensus(viewport.vconsensus);
+      if (cs.conservationApplied())
+      {
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
+
+        cs.setConservation(c);
+      }
+    }
+
+    int s, sSize = viewport.alignment.getGroups().size();
+    for(s=0; s<sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+      }
+      sg.recalcConservation();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
@@ -716,15 +1095,18 @@ public class AlignFrame
 
       if (current.getLength() < Width)
       {
-        current.insertCharAt(Width-1, viewport.getGapCharacter());
+        current.insertCharAt(Width - 1, viewport.getGapCharacter());
       }
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    alignmentChanged();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     JInternalFrame frame = new JInternalFrame();
@@ -734,11 +1116,21 @@ public class AlignFrame
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void font_actionPerformed(ActionEvent e)
   {
     FontChooser fc = new FontChooser(alignPanel);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void fullSeqId_actionPerformed(ActionEvent e)
   {
     viewport.setShowFullId(fullSeqId.isSelected());
@@ -747,12 +1139,22 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.isSelected());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setWrapAlignment(wrapMenuItem.isSelected());
@@ -763,42 +1165,77 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText(viewTextMenuItem.isSelected());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
   public void sequenceFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
@@ -815,6 +1252,11 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
     if (annotationPanelMenuItem.isSelected() &&
@@ -829,6 +1271,11 @@ public class AlignFrame
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
     if (alignPanel.overviewPanel != null)
@@ -856,124 +1303,170 @@ public class AlignFrame
     alignPanel.setOverviewPanel(overview);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
     changeColour(null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void clustalColour_actionPerformed(ActionEvent e)
   {
     changeColour(new ClustalxColourScheme(
         viewport.alignment.getSequences(), viewport.alignment.getWidth()));
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void zappoColour_actionPerformed(ActionEvent e)
   {
     changeColour(new ZappoColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void taylorColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TaylorColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
     changeColour(new HydrophobicColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void helixColour_actionPerformed(ActionEvent e)
   {
     changeColour(new HelixColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void strandColour_actionPerformed(ActionEvent e)
   {
     changeColour(new StrandColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void turnColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TurnColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void buriedColour_actionPerformed(ActionEvent e)
   {
     changeColour(new BuriedColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void nucleotideColour_actionPerformed(ActionEvent e)
   {
     changeColour(new NucleotideColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cs DOCUMENT ME!
+   */
   void changeColour(ColourSchemeI cs)
   {
     int threshold = 0;
 
-    if (viewport.getAbovePIDThreshold())
+    if(cs!=null)
     {
-      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                                                 "Background");
-
-      if (cs instanceof ResidueColourScheme)
+      if (viewport.getAbovePIDThreshold())
       {
-        ( (ResidueColourScheme) cs).setThreshold(threshold);
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                                                   "Background");
+
+        cs.setThreshold(threshold,
+                        viewport.getIgnoreGapsConsensus());
+
+        viewport.setGlobalColourScheme(cs);
       }
-      else if (cs instanceof ScoreColourScheme)
+      else
       {
-        ( (ScoreColourScheme) cs).setThreshold(threshold);
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
       }
 
-      viewport.setGlobalColourScheme(cs);
-    }
-    else if (cs instanceof ResidueColourScheme)
-    {
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      ( (ScoreColourScheme) cs).setThreshold(0);
-    }
-
-    if (viewport.getConservationSelected())
-    {
-      ConservationColourScheme ccs = null;
-
-      Alignment al = (Alignment) viewport.alignment;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth() - 1);
+      if (viewport.getConservationSelected())
+      {
 
-      c.calculate();
-      c.verdict(false, viewport.ConsPercGaps);
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
 
-      ccs = new ConservationColourScheme(c, cs);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
 
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus(viewport.vconsensus);
-      viewport.setGlobalColourScheme(ccs);
+        cs.setConservation(c);
 
-      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
-                                                  "Background");
-    }
-    else
-    {
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      if (cs != null)
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
+      }
+      else
       {
-        cs.setConsensus(viewport.vconsensus);
+        cs.setConservation(null);
       }
 
-      viewport.setGlobalColourScheme(cs);
+      cs.setConsensus(viewport.vconsensus);
     }
 
+    viewport.setGlobalColourScheme(cs);
+
     if (viewport.getColourAppliesToAllGroups())
     {
       Vector groups = viewport.alignment.getGroups();
@@ -985,8 +1478,10 @@ public class AlignFrame
         if (cs == null)
         {
           sg.cs = null;
+          continue;
         }
-        else if (cs instanceof ClustalxColourScheme)
+
+        if (cs instanceof ClustalxColourScheme)
         {
           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
@@ -1005,20 +1500,19 @@ public class AlignFrame
           }
         }
 
-        if (viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
         {
-          if (sg.cs instanceof ResidueColourScheme)
-          {
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-          }
-          else if (sg.cs instanceof ScoreColourScheme)
-          {
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-          }
+         sg.cs.setThreshold(threshold,
+                viewport.getIgnoreGapsConsensus());
 
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
               sg.getWidth()));
         }
+        else
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+
 
         if (viewport.getConservationSelected())
         {
@@ -1028,21 +1522,10 @@ public class AlignFrame
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
-
-          ConservationColourScheme ccs = new ConservationColourScheme(c,
-              sg.cs);
-
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                                 sg.getWidth()));
-          sg.cs = ccs;
-        }
-        else if (cs != null)
-        {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-              sg.getWidth()));
+          sg.cs.setConservation(c);
         }
+        else
+          sg.cs.setConservation(null);
       }
     }
 
@@ -1054,9 +1537,14 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold())
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
                                      viewport.getGlobalColourScheme(),
@@ -1065,9 +1553,14 @@ public class AlignFrame
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected())
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setConservationSlider(alignPanel,
                                         viewport.globalColourScheme,
@@ -1076,6 +1569,11 @@ public class AlignFrame
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -1083,20 +1581,16 @@ public class AlignFrame
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyConservation_actionPerformed(null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -1106,33 +1600,122 @@ public class AlignFrame
 
     ColourSchemeI cs = viewport.getGlobalColourScheme();
 
-    if (cs instanceof ConservationColourScheme)
+    changeColour(viewport.getGlobalColourScheme());
+
+    modifyPID_actionPerformed(null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void userDefinedColour_actionPerformed(ActionEvent e)
+  {
+    if (e.getActionCommand().equals("User Defined..."))
     {
-      changeColour( ( (ConservationColourScheme) cs).cs);
+      new UserDefinedColours(alignPanel, null);
     }
     else
     {
-      changeColour(cs);
-    }
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+          getUserColourSchemes().get(e.getActionCommand());
 
-    modifyPID_actionPerformed(null);
+      changeColour(udc);
+    }
   }
 
-  public void userDefinedColour_actionPerformed(ActionEvent e)
+  public void updateUserColourMenu()
   {
-    new UserDefinedColours(alignPanel, null);
+
+    Component[] menuItems = colourMenu.getMenuComponents();
+    int i, iSize = menuItems.length;
+    for (i = 0; i < iSize; i++)
+    {
+      if (menuItems[i].getName() != null &&
+          menuItems[i].getName().equals("USER_DEFINED"))
+      {
+        colourMenu.remove(menuItems[i]);
+        iSize--;
+      }
+    }
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+            nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+            {
+              public void mousePressed(MouseEvent evt)
+              {
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                {
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
+                  if(option == JOptionPane.YES_OPTION)
+                  {
+                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+                    colourMenu.remove(radioItem);
+                  }
+                  else
+                    radioItem.addActionListener(new ActionListener()
+                    {
+                      public void actionPerformed(ActionEvent evt)
+                      {
+                        userDefinedColour_actionPerformed(evt);
+                      }
+                    });
+                }
+              }
+            });
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+
+        colourMenu.insert(radioItem, 15);
+        colours.add(radioItem);
+      }
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void PIDColour_actionPerformed(ActionEvent e)
   {
     changeColour(new PIDColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
     changeColour(new Blosum62ColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
@@ -1142,6 +1725,11 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
@@ -1150,16 +1738,25 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
                                    HistoryItem.SORT));
 
-    //  AlignmentSorter.sortByGroup(viewport.getAlignment());
-    AlignmentSorter.sortGroups(viewport.getAlignment());
+    AlignmentSorter.sortByGroup(viewport.getAlignment());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
     RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
@@ -1169,6 +1766,11 @@ public class AlignFrame
                              100, false);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if ( (viewport.getSelectionGroup() == null) ||
@@ -1187,6 +1789,11 @@ public class AlignFrame
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
     if ( ( (viewport.getSelectionGroup() != null) &&
@@ -1220,26 +1827,53 @@ public class AlignFrame
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "PID", "Average distance tree using PID");
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param type DOCUMENT ME!
+   * @param pwType DOCUMENT ME!
+   * @param title DOCUMENT ME!
+   */
   void NewTreePanel(String type, String pwType, String title)
   {
     final TreePanel tp;
@@ -1299,6 +1933,12 @@ public class AlignFrame
     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param title DOCUMENT ME!
+   * @param order DOCUMENT ME!
+   */
   public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
   {
     final JMenuItem item = new JMenuItem("by " + title);
@@ -1317,6 +1957,15 @@ public class AlignFrame
     });
   }
 
+  /**
+   * Maintain the Order by->Displayed Tree menu.
+   * Creates a new menu item for a TreePanel with an appropriate
+   * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
+   * to remove the menu item when the treePanel is closed, and adjust
+   * the tree leaf to sequence mapping when the alignment is modified.
+   * @param treePanel Displayed tree window.
+   * @param title SortBy menu item title.
+   */
   void addTreeMenuItem(final TreePanel treePanel, String title)
   {
     final JMenuItem item = new JMenuItem(title);
@@ -1370,50 +2019,13 @@ public class AlignFrame
     });
   }
 
-  public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-    // TODO:resolve which menu item was actually selected
-    // Now, check we have enough sequences
-    SequenceI[] msa = null;
-
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 1))
-    {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
-      int sz;
-      msa = new SequenceI[sz = seqs.getSize()];
-
-      for (int i = 0; i < sz; i++)
-      {
-        msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      }
-    }
-    else
-    {
-      Vector seqs = viewport.getAlignment().getSequences();
-
-      if (seqs.size() > 1)
-      {
-        msa = new SequenceI[seqs.size()];
-
-        for (int i = 0; i < seqs.size(); i++)
-        {
-          msa[i] = (SequenceI) seqs.elementAt(i);
-        }
-      }
-    }
-
-    if (msa != null)
-    {
-      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
-          title, msa, false, true);
-    }
-  }
-
-  public void ClustalRealign_actionPerformed(ActionEvent e)
+  /**
+   * Work out whether the whole set of sequences
+   * or just the selected set will be submitted for multiple alignment.
+   *
+   */
+  private SequenceI[] gatherSequencesForAlignment()
   {
-    // TODO:resolve which menu item was actually selected
     // Now, check we have enough sequences
     SequenceI[] msa = null;
 
@@ -1444,15 +2056,16 @@ public class AlignFrame
         }
       }
     }
-
-    if (msa != null)
-    {
-      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
-          title, msa, true, true);
-    }
+    return msa;
   }
 
-  protected void jpred_actionPerformed(ActionEvent e)
+  /**
+   * Decides what is submitted to a secondary structure prediction service,
+   * the currently selected sequence, or the currently selected alignment
+   * (where the first sequence in the set is the one that the prediction
+   * will be for).
+   */
+  SequenceI[] gatherSeqOrMsaForSecStrPrediction()
   {
     SequenceI seq = null;
     SequenceI[] msa = null;
@@ -1496,63 +2109,26 @@ public class AlignFrame
         }
       }
     }
-
     if (msa != null)
     {
-      JPredClient ct = new JPredClient(title, msa);
-    }
-    else if (seq != null)
-    {
-      JPredClient ct = new JPredClient(title, seq);
-    }
-    else
-    {
-      System.err.print(
-          "JALVIEW ERROR! - Unexpected JPred selection state!\n");
-    }
-  }
-
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-    // TODO:resolve which menu item was actually selected
-    // Now, check we have enough sequences
-    SequenceI[] msa = null;
-
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 1))
-    {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
-      int sz;
-      msa = new SequenceI[sz = seqs.getSize()];
-
-      for (int i = 0; i < sz; i++)
-      {
-        msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      }
+      return msa;
     }
     else
     {
-      Vector seqs = viewport.getAlignment().getSequences();
-
-      if (seqs.size() > 1)
+      if (seq != null)
       {
-        msa = new SequenceI[seqs.size()];
-
-        for (int i = 0; i < seqs.size(); i++)
-        {
-          msa[i] = (SequenceI) seqs.elementAt(i);
-        }
+        return new SequenceI[]
+            {
+            seq};
       }
     }
-
-    if (msa != null)
-    {
-      MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
-                                                  false, true);
-    }
+    return null;
   }
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -1574,7 +2150,7 @@ public class AlignFrame
       {
         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
             "File");
-        viewport.setCurrentTree( ShowNewickTree(fin, choice).getTree() );
+        viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
       }
       catch (Exception ex)
       {
@@ -1587,19 +2163,41 @@ public class AlignFrame
     }
   }
 
+
   public TreePanel ShowNewickTree(NewickFile nf, String title)
   {
+    return ShowNewickTree(nf,title,600,500,4,5);
+  }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param nf DOCUMENT ME!
+   * @param title DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
+  {
     TreePanel tp = null;
+
     try
     {
       nf.parse();
+
       if (nf.getTree() != null)
       {
         tp = new TreePanel(viewport,
-                                     viewport.getAlignment().getSequences(), nf,
-                                     "FromFile",
-                                     title);
-        Desktop.addInternalFrame(tp, title, 600, 500);
+                           viewport.getAlignment().getSequences(), nf,
+                           "FromFile",
+                           title);
+
+        tp.setSize(w,h);
+
+        if(x>0 && y>0)
+          tp.setLocation(x,y);
+
+
+        Desktop.addInternalFrame(tp, title, w, h);
         addTreeMenuItem(tp, title);
       }
     }
@@ -1607,6 +2205,7 @@ public class AlignFrame
     {
       ex.printStackTrace();
     }
+
     return tp;
   }
 
@@ -1632,4 +2231,111 @@ public class AlignFrame
       }
     }
   }
+
+  /**
+   * Generates menu items and listener event actions for web service clients
+   *
+   */
+  public void BuildWebServiceMenu()
+  {
+    if ( (Desktop.discoverer.services != null)
+        && (Desktop.discoverer.services.size() > 0))
+    {
+      Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
+      Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
+      Vector wsmenu = new Vector();
+      if (msaws != null)
+      {
+        // Add any Multiple Sequence Alignment Services
+        final JMenu msawsmenu = new JMenu("Alignment");
+        for (int i = 0, j = msaws.size(); i < j; i++)
+        {
+          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
+              get(i);
+          final JMenuItem method = new JMenuItem(sh.getName());
+          method.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              SequenceI[] msa = gatherSequencesForAlignment();
+              MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
+                  false, true);
+
+            }
+
+          });
+          msawsmenu.add(method);
+          // Deal with services that we know accept partial alignments.
+          if (sh.getName().indexOf("lustal") > -1)
+          {
+            // We know that ClustalWS can accept partial alignments for refinement.
+            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
+            methodR.addActionListener(new ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                SequenceI[] msa = gatherSequencesForAlignment();
+                MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
+                    true, true);
+
+              }
+
+            });
+            msawsmenu.add(methodR);
+
+          }
+        }
+        wsmenu.add(msawsmenu);
+      }
+      if (secstrpr != null)
+      {
+        // Add any secondary structure prediction services
+        final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
+        for (int i = 0, j = secstrpr.size(); i < j; i++)
+        {
+          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
+              secstrpr.get(i);
+          final JMenuItem method = new JMenuItem(sh.getName());
+          method.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
+              if (msa.length == 1)
+              {
+                // Single Sequence prediction
+                jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
+                    title, msa[0]);
+              }
+              else
+              {
+                if (msa.length > 1)
+                {
+                  // Single Sequence prediction
+                  jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
+                      title, msa);
+                }
+              }
+            }
+          });
+          secstrmenu.add(method);
+        }
+        wsmenu.add(secstrmenu);
+      }
+      this.webService.removeAll();
+      for (int i = 0, j = wsmenu.size(); i < j; i++)
+      {
+        webService.add( (JMenu) wsmenu.get(i));
+      }
+    }
+    else
+    {
+      this.webService.removeAll();
+      this.webService.add(this.webServiceNoServices);
+    }
+    // TODO: add in rediscovery function
+    // TODO: reduce code redundancy.
+    // TODO: group services by location as well as function.
+  }
+
 }