X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=725a702da877fce68aab0c669e68abaa7f32be87;hb=67fe33692d163752fd467468b18ace4a9b4eac7d;hp=a977623a7becdaff27bc068a4582ebbe911d524e;hpb=edd50f0798768bc48fc0ae7be6401db6c925d06a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a977623..725a702 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -16,38 +16,81 @@ import jalview.schemes.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
-import MCview.*;
+import jalview.ws.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
+import javax.swing.event.*;
 import java.util.*;
+import java.awt.datatransfer.*;
+
 
 public class AlignFrame extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
+  public static final int NEW_WINDOW_WIDTH = 700;
+  public static final int NEW_WINDOW_HEIGHT = 500;
+  public String currentFileFormat = "Jalview";
+
   public AlignFrame(AlignmentI al)
   {
-    super();
-    viewport = new AlignViewport(al,true,true,true,false);
+    viewport = new AlignViewport(al);
+
     alignPanel = new AlignmentPanel(this, viewport);
+    alignPanel.annotationPanel.adjustPanelHeight();
+    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
+
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
-    fontNameMenuItem.setText(viewport.getFont().getName());
-    fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
+
+    addInternalFrameListener(new InternalFrameAdapter()
+   {
+     public void internalFrameActivated(InternalFrameEvent evt)
+     {
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {      alignPanel.requestFocus();    }
+          });
+
+     }
+   });
+
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
-    chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
+        ,  new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},
+          new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
+          currentFileFormat);
+
+    chooser.setAcceptAllFileFilterUsed(false);
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
-    if(value == JFileChooser.APPROVE_OPTION)
+    if(value == JalviewFileChooser.APPROVE_OPTION)
     {
+      currentFileFormat  = chooser.getSelectedFormat();
+
+      if (currentFileFormat.equals("Jalview"))
+      {
+        String shortName = title.replace('/', '_');
+        title = title.replace('\\', '_');
+        String choice = chooser.getSelectedFile().getPath();
+        Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,
+                              choice);
+        // USE Jalview2XML to save this file
+        return;
+      }
+
       String choice =  chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.LAST_DIRECTORY = choice;
-      String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
       try{
         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
         out.println(output);
@@ -65,15 +108,26 @@ public class AlignFrame extends GAlignFrame
      cap.formatForOutput();
      frame.setContentPane(cap);
      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
-     cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
+     cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
   }
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
+    HTMLOutput htmlOutput = new HTMLOutput(viewport);
     htmlOutput = null;
   }
 
+  protected void createPNG_actionPerformed(ActionEvent e)
+  {
+    alignPanel.makePNG();
+  }
+
+  protected void epsFile_actionPerformed(ActionEvent e)
+  {
+    alignPanel.makeEPS();
+  }
+
+
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     //Putting in a thread avoids Swing painting problems
@@ -113,8 +167,8 @@ public class AlignFrame extends GAlignFrame
     }catch(Exception ex){}
   }
 
-  ArrayList  historyList = new ArrayList();
-  ArrayList redoList = new ArrayList();
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
 
   void updateEditMenuBar()
   {
@@ -147,6 +201,7 @@ public class AlignFrame extends GAlignFrame
   {
     // must make sure we add new sequence objects her, not refs to the existing sequences
     redoList.clear();
+
     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
     for(int i=0; i<viewport.getAlignment().getHeight(); i++)
     {
@@ -154,6 +209,7 @@ public class AlignFrame extends GAlignFrame
                              viewport.getAlignment().getSequenceAt(i).getSequence());
     }
 
+
     historyList.add(0, new Object[]{type,  seq} );
     updateEditMenuBar();
   }
@@ -174,103 +230,254 @@ public class AlignFrame extends GAlignFrame
     redoList.add(0, new Object[] {history[0], seq});
 
       seq = (SequenceI[]) history[1];
+      AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
       viewport.setAlignment( new Alignment(seq) );
+      viewport.alignment.setGapCharacter( Preferences.gapSymbol );
       updateEditMenuBar();
-      alignPanel.RefreshPanels();
+      for(int i=0; i<old.length; i++)
+        viewport.alignment.addAnnotation(old[i]);
+      viewport.updateConsensus();
+      viewport.updateConservation();
+      alignPanel.repaint();
   }
 
-
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  public void moveSelectedSequences(boolean up)
   {
-     Object [] history = (Object[])redoList.remove(0);
-     SequenceI[] seq = (SequenceI[]) history[1];
-     viewport.setAlignment( new Alignment(seq) );
-     updateEditMenuBar();
-     alignPanel.RefreshPanels();
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg == null)
+      return;
+
+    if (up)
+    {
+      for (int i = 1; i < viewport.alignment.getHeight(); i++)
+      {
+        SequenceI seq = viewport.alignment.getSequenceAt(i);
+        if (!sg.sequences.contains(seq))
+          continue;
+
+        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+        if (sg.sequences.contains(temp))
+          continue;
+
+        viewport.alignment.getSequences().setElementAt(temp, i);
+        viewport.alignment.getSequences().setElementAt(seq, i - 1);
+      }
+    }
+    else
+    {
+      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+      {
+        SequenceI seq = viewport.alignment.getSequenceAt(i);
+        if (!sg.sequences.contains(seq))
+          continue;
+
+        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+        if (sg.sequences.contains(temp))
+          continue;
+
+        viewport.alignment.getSequences().setElementAt(temp, i);
+        viewport.alignment.getSequences().setElementAt(seq, i + 1);
+      }
+    }
+
+    alignPanel.repaint();
   }
 
 
 
-  public void groupsMenuItem_actionPerformed(ActionEvent e)
+  protected void copy_actionPerformed(ActionEvent e)
   {
-    GroupEditor geditor = new GroupEditor(viewport, alignPanel);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(geditor);
-    Desktop.addInternalFrame(frame, "Group editor", 710, 410);
-    frame.setResizable(false);
+     if(viewport.getSelectionGroup()==null)
+       return;
+
+     SequenceGroup sg = viewport.getSelectionGroup();
+
+     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+     StringBuffer buffer= new StringBuffer();
+
+     Hashtable orderedSeqs = new Hashtable();
+     for(int i=0; i<sg.getSize(); i++)
+     {
+        SequenceI seq = sg.getSequenceAt(i);
+        int index = viewport.alignment.findIndex(seq);
+        orderedSeqs.put(index+"", seq);
+     }
+
+     int index=0;
+     for(int i=0; i<sg.getSize(); i++)
+     {
+       SequenceI seq = null;
+       while( seq == null )
+       {
+         if(orderedSeqs.containsKey(index+""))
+         {
+           seq = (SequenceI) orderedSeqs.get(index + "");
+           index++;
+           break;
+         }
+         else
+           index++;
+       }
+
+         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");
+     }
+     c.setContents( new StringSelection( buffer.toString()) , null ) ;
+
   }
 
-  public void groupEditingMenuItem_actionPerformed(ActionEvent e)
+
+  protected void pasteNew_actionPerformed(ActionEvent e)
   {
-    viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
+    paste(true);
   }
 
-  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sel.addElement( viewport.getAlignment().getSequenceAt(i));
-    PaintRefresher.Refresh(null);
+    addHistoryItem("Paste");
+    paste(false);
   }
 
-  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  void paste(boolean newAlignment)
   {
-    viewport.getSelection().clear();
-    PaintRefresher.Refresh(null);
+    try{
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
+      if (contents == null)
+        return;
+
+      String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+      StringTokenizer st = new StringTokenizer(str);
+      ArrayList seqs = new ArrayList();
+      while (st.hasMoreElements())
+      {
+        String name = st.nextToken();
+        int start = Integer.parseInt(st.nextToken());
+        int end = Integer.parseInt(st.nextToken());
+        Sequence sequence = new Sequence(name,st.nextToken(), start, end);
+
+        if(!newAlignment)
+          viewport.alignment.addSequence(sequence);
+        else
+          seqs.add(sequence);
+      }
+
+      if(newAlignment)
+      {
+        SequenceI[] newSeqs = new SequenceI[seqs.size()];
+        seqs.toArray(newSeqs);
+        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+        String newtitle = new String("Copied sequences");
+        if( title.startsWith("Copied sequences"))
+         newtitle = title;
+       else
+         newtitle = newtitle.concat("- from "+title);
+
+        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+      }
+      else
+      {
+        viewport.setEndSeq(viewport.alignment.getHeight());
+        viewport.alignment.getWidth();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
+      }
+
+    }catch(Exception ex){}// could be anything being pasted in here
+
   }
 
-  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+
+  protected void cut_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-    {
-      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
-        sel.removeElement(viewport.getAlignment().getSequenceAt(i));
-      else
-        sel.addElement(viewport.getAlignment().getSequenceAt(i));
-    }
-    PaintRefresher.Refresh(null);
+    copy_actionPerformed(null);
+    delete_actionPerformed(null);
   }
 
-  public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
+  protected void delete_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete selection");
+    addHistoryItem("Delete");
+    if (viewport.getSelectionGroup() == null)
+      return;
+
+     SequenceGroup sg = viewport.getSelectionGroup();
+     for (int i=0;i < sg.sequences.size(); i++)
+     {
+       SequenceI seq = sg.getSequenceAt(i);
+       int index = viewport.getAlignment().findIndex(seq);
+       seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
+
+       if(seq.getSequence().length()<1)
+          viewport.getAlignment().deleteSequence(seq);
+      else
+          viewport.getAlignment().getSequences().setElementAt(seq, index);
+     }
+
+     viewport.setSelectionGroup(null);
+     viewport.alignment.deleteGroup(sg);
+     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
+     if(viewport.getAlignment().getHeight()<1)
+     try
+     {
+       this.setClosed(true);
+     }catch(Exception ex){}
+   viewport.updateConservation();
+   viewport.updateConsensus();
+     alignPanel.repaint();
+
+  }
 
-    for (int i=0;i < viewport.getSelection().size(); i++)
-            viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
 
-    viewport.getSelection().clear();
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
-    alignPanel.RefreshPanels();
+
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+     Object [] history = (Object[])redoList.remove(0);
+     SequenceI[] seq = (SequenceI[]) history[1];
+     viewport.setAlignment( new Alignment(seq) );
+     viewport.alignment.setGapCharacter( Preferences.gapSymbol );
+     updateEditMenuBar();
+     viewport.updateConsensus();
+     alignPanel.repaint();
+     alignPanel.repaint();
   }
 
-  public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
+
+  protected void deleteGroups_actionPerformed(ActionEvent e)
   {
-    copySelectedMenuItem_actionPerformed(null);
-    deleteSelectedMenuItem_actionPerformed(null);
+    viewport.alignment.deleteAllGroups();
+    viewport.setSelectionGroup(null);
     alignPanel.repaint();
   }
 
-  public void copySelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    if(viewport.getSelection().size()==0)
-      return;
 
-   SequenceI[] s = new Sequence[viewport.getSelection().size()];
-   for (int i=0; i < viewport.getSelection().size(); i++) {
-     s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
-    }
-    AlignFrame af = new AlignFrame(new Alignment(s));
-    int newHeight = s.length * af.viewport.getCharHeight() + 200;
-    if(newHeight>500)
-      newHeight=500;
-    Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
+
+  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = new SequenceGroup();
+    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+    sg.setEndRes(viewport.alignment.getWidth());
+    viewport.setSelectionGroup(sg);
+    PaintRefresher.Refresh(null);
   }
 
-  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
+  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
+    viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
-    repaint();
+    viewport.setSelectionGroup(null);
+    PaintRefresher.Refresh(null);
+  }
+
+  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
+
+    PaintRefresher.Refresh(null);
   }
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
@@ -282,7 +489,19 @@ public class AlignFrame extends GAlignFrame
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0,min);
-      alignPanel.RefreshPanels();
+
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveLeft(min))
+          viewport.alignment.deleteGroup(sg);
+      }
+
+      alignPanel.repaint();
     }
   }
 
@@ -293,10 +512,21 @@ public class AlignFrame extends GAlignFrame
     if (colSel.size() > 0)
     {
       int max = colSel.getMax();
-      if(max>1)
-        viewport.getAlignment().trimRight(max);
+      viewport.getAlignment().trimRight(max);
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveRight(max))
+          viewport.alignment.deleteGroup(sg);
+      }
 
-      alignPanel.RefreshPanels();
+
+
+      alignPanel.repaint();
     }
 
   }
@@ -305,7 +535,9 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
-    alignPanel.RefreshPanels();
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -318,326 +550,402 @@ public class AlignFrame extends GAlignFrame
       current = viewport.getAlignment().getSequenceAt(i);
       jSize = current.getLength();
       for (int j=0; j < jSize; j++)
-        if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
+        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
           current.deleteCharAt(j);
           j--;
           jSize--;
         }
     }
-
-    alignPanel.RefreshPanels();
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
   }
 
-  public void setGapCharMenuItem_actionPerformed(ActionEvent e)
-  {
-    char thisChar = '-';
-    char nextChar = '.';
-    if(viewport.getGapCharacter()=='-')
-    {
-      thisChar = '.';
-      nextChar = '-';
-    }
-    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
-    viewport.setGapCharacter(thisChar);
-    alignPanel.RefreshPanels();
-  }
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane op = new JOptionPane();
-    JInternalFrame frame =  op.createInternalFrame(this, "Find");
+    JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
     frame.setContentPane(finder);
-    frame.setSize(300,110);
-    frame.setVisible(true);
-  }
+    Desktop.addInternalFrame(frame, "Find", 340,110);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
+  }
 
 
-  public void fontNameMenuItem_actionPerformed(ActionEvent e)
+  public void font_actionPerformed(ActionEvent e)
   {
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-
+    FontChooser fc = new FontChooser( alignPanel );
+  }
 
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font",
-                                "Font selection",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null,fonts
-                                ,fontNameMenuItem.getText()).toString();
-    if(selection!=null)
-    {
-       fontNameMenuItem.setText(selection);
-       SetFont();
-     }
+  protected void fullSeqId_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowFullId( fullSeqId.isSelected() );
 
+    alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
+    alignPanel.repaint();
   }
 
-  public void fontSizeMenuItem_actionPerformed(ActionEvent e)
+  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font size",
-                                "Font size",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
-                                ,fontSizeMenuItem.getText()).toString();
-    if(selection!=null)
-     {
-       fontSizeMenuItem.setText(selection);
-       SetFont();
-     }
+      viewport.setColourText( colourTextMenuItem.isSelected() );
+      alignPanel.repaint();
   }
 
-  public void fontStyleMenuItem_actionPerformed(ActionEvent e)
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font style",
-                                "Font style",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null, new String[]{"plain", "bold", "italic"}
-                                ,fontStyleMenuItem.getText()).toString();
-    if(selection!=null)
-    {
-      fontStyleMenuItem.setText(selection);
-      SetFont();
-    }
-
+    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
+    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+    scaleAbove.setVisible( wrapMenuItem.isSelected() );
+    scaleLeft.setVisible( wrapMenuItem.isSelected() );
+    scaleRight.setVisible( wrapMenuItem.isSelected() );
+    alignPanel.repaint();
   }
 
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  protected void scaleAbove_actionPerformed(ActionEvent e)
   {
-      updateResidueView();
+    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+    alignPanel.repaint();
   }
 
-  void SetFont()
+  protected void scaleLeft_actionPerformed(ActionEvent e)
   {
-      int style = java.awt.Font.PLAIN;
-      if(fontStyleMenuItem.getText().equals("bold"))
-        style = java.awt.Font.BOLD;
-      else if(fontStyleMenuItem.getText().equals("italic"))
-        style = java.awt.Font.ITALIC;
-
-      viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
-                                           style,
-                                           Integer.parseInt(fontSizeMenuItem.getText())));
-      alignPanel.RefreshPanels();
-
+    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.repaint();
   }
 
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  protected void scaleRight_actionPerformed(ActionEvent e)
   {
-     updateResidueView();
+    viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.repaint();
   }
 
 
+
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-     updateResidueView();
+    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
+    alignPanel.repaint();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-     updateResidueView();
+    viewport.setShowText( viewTextMenuItem.isSelected() );
+    alignPanel.repaint();
   }
 
 
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
-
-  void updateResidueView()
+  public void sequenceFeatures_actionPerformed(ActionEvent evt)
   {
-    if (viewport.getSelection().size() == 0)
-     {
-       for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
-       {
-         SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
-         sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
-         sg.setDisplayText( viewTextMenuItem.isSelected() );
-         sg.setColourText( colourTextMenuItem.isSelected() );
-       }
-     }
-     else
-     {
-       SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
-       if (alignPanel.seqPanel.isNewSelection(sg))
-       {
-         sg = viewport.getAlignment().addGroup();
-         for (int i = 0; i < viewport.getSelection().size(); i++)
-         {
-           viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
-               Sequence) viewport.sel.sequenceAt(i)),
-                                              (Sequence) viewport.sel.sequenceAt(
-               i));
-           viewport.alignment.addToGroup(sg,
-                                         (Sequence) viewport.sel.sequenceAt(i));
-         }
-       }
-
-       sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
-       sg.setDisplayText(viewTextMenuItem.isSelected());
-       sg.setColourText(colourTextMenuItem.isSelected());
-     }
-    alignPanel.RefreshPanels();
+    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
+    if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+    {
+         SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
+         ((Alignment)viewport.alignment).featuresAdded = true;
+    }
+    alignPanel.repaint();
   }
 
-
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
+    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+    {
+      annotationPanelMenuItem.setSelected(false);
+      return;
+    }
+    viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
+    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    if (alignPanel.overviewPanel != null)
+      return;
 
     JInternalFrame frame = new JInternalFrame();
-    OverviewPanel overview = alignPanel.getOverviewPanel();
-   try{
-     overview = new OverviewPanel(alignPanel, viewport);
+    OverviewPanel overview = new OverviewPanel(alignPanel);
      frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
                              frame.getWidth(), frame.getHeight());
     frame.pack();
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
       {
             alignPanel.setOverviewPanel(null);
       };
     });
-    alignPanel.setOverviewPanel( overview );
 
-  }catch(java.lang.OutOfMemoryError ex)
-   {
-     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
-                                   +"\nTry reducing the font size.",
-                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
-   }
+    alignPanel.setOverviewPanel( overview );
 
 
   }
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme(null, false);
+    changeColour( null );
   }
 
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-   // alignPanel.setColourScheme( new ClustalxColourScheme() );
+    abovePIDThreshold.setSelected(false);
+    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );
+    changeColour(new ZappoColourScheme());
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );
+    changeColour(new TaylorColourScheme());
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );
+    changeColour( new HydrophobicColourScheme() );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );
+    changeColour(new HelixColourScheme() );
   }
 
 
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );
+    changeColour(new StrandColourScheme());
   }
 
 
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );
+    changeColour(new TurnColourScheme());
   }
 
 
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );
+    changeColour(new BuriedColourScheme() );
+  }
+
+  public void nucleotideColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new NucleotideColourScheme());
   }
 
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );
-    conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
+    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
   }
 
 
 
-  public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
- {
-   ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
-   JInternalFrame frame = new JInternalFrame();
-   frame.setContentPane(cip);
-   Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
-   frame.setMaximizable(false);
- }
+  void changeColour(ColourSchemeI cs)
+  {
+    int threshold = 0;
+
+    if ( viewport.getAbovePIDThreshold() )
+    {
+      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
+
+      if (cs instanceof ResidueColourScheme)
+        ( (ResidueColourScheme) cs).setThreshold(threshold);
+      else if (cs instanceof ScoreColourScheme)
+        ( (ScoreColourScheme) cs).setThreshold(threshold);
+
+      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);
+
+      c.calculate();
+      c.verdict(false, viewport.ConsPercGaps);
 
+      ccs = new ConservationColourScheme(c, cs);
 
-  public void abovePIDColour_actionPerformed(ActionEvent e)
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      ccs.setConsensus( viewport.vconsensus );
+      viewport.setGlobalColourScheme(ccs);
+
+      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+
+    }
+    else
+    {
+        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+        if (cs != null)
+          cs.setConsensus(viewport.vconsensus);
+        viewport.setGlobalColourScheme(cs);
+    }
+
+
+    if(viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+        }
+        else if(cs!=null)
+        {
+          try{
+            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+          }catch(Exception ex){ex.printStackTrace();}
+        }
+
+        if(viewport.getAbovePIDThreshold())
+        {
+          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.sequences, 0, sg.getWidth()) );
+        }
+
+        if( viewport.getConservationSelected() )
+        {
+          Conservation c = new Conservation("Group",
+                                            ResidueProperties.propHash, 3,
+                                            sg.sequences, 0, 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()));
+        }
+
+      }
+    }
+
+    if(alignPanel.getOverviewPanel()!=null)
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    alignPanel.repaint();
+  }
+
+  protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );
+      if(viewport.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                   "Background");
+        SliderPanel.showPIDSlider();
+      }
   }
 
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+    if(viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
+                                        "Background");
+      SliderPanel.showConservationSlider();
+    }
+  }
 
-  public void userDefinedColour_actionPerformed(ActionEvent e)
+
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+    viewport.setAbovePIDThreshold(false);
+    abovePIDThreshold.setSelected(false);
+
+   ColourSchemeI cs = viewport.getGlobalColourScheme();
+   if(cs instanceof ConservationColourScheme )
+     changeColour( ((ConservationColourScheme)cs).cs );
+    else
+      changeColour( cs );
+
+    modifyConservation_actionPerformed(null);
   }
 
-  public void PIDColour_actionPerformed(ActionEvent e)
+  public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+    conservationMenuItem.setSelected(false);
+    viewport.setConservationSelected(false);
+
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+
+    if(cs instanceof ConservationColourScheme )
+        changeColour( ((ConservationColourScheme)cs).cs );
+    else
+        changeColour( cs );
+
+    modifyPID_actionPerformed(null);
   }
 
 
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+
+  public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );
+    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
   }
 
+  public void PIDColour_actionPerformed(ActionEvent e)
+  {
+    changeColour( new PIDColourScheme() );
+  }
 
 
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
+  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
-    Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
+    changeColour(new Blosum62ColourScheme() );
   }
 
 
+
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("sort");
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("sort");
     AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
@@ -645,27 +953,21 @@ public class AlignFrame extends GAlignFrame
     addHistoryItem("sort");
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
-  }
-
-  public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    if(viewport.getCurrentTree()==null)
-      return;
-
-    AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
+    RedundancyPanel sp = new RedundancyPanel(alignPanel);
+    JInternalFrame frame = new JInternalFrame();
+    frame.setContentPane(sp);
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
 
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelection().size()<2)
+    if(viewport.getSelectionGroup().getSize()<2)
       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
     else
     {
@@ -677,7 +979,8 @@ public class AlignFrame extends GAlignFrame
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
+
+    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
        || viewport.getAlignment().getHeight()<4)
     {
       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
@@ -724,72 +1027,230 @@ public class AlignFrame extends GAlignFrame
 
   void NewTreePanel(String type, String pwType, String title)
   {
-    JInternalFrame frame = new javax.swing.JInternalFrame();
-    TreePanel tp=null;
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
-   {
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
-                         viewport.getStartRes(), viewport.getEndRes());
-   }
-   else
-   {
-     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, viewport.getStartRes(),
-                         viewport.getEndRes());
-   }
+    //are the sequences aligned?
+    if(!viewport.alignment.isAligned())
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
+                                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+      return;
+    }
+
+    final TreePanel tp;
+    if (viewport.getSelectionGroup() != null &&
+        viewport.getSelectionGroup().getSize() > 3)
+    {
+      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
+                         pwType,
+                         0, viewport.alignment.getWidth());
+    }
+    else
+    {
+      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                         type, pwType, 0, viewport.alignment.getWidth());
+    }
+
+   addTreeMenuItem(tp, title);
 
-   frame.setContentPane(tp);
-   Desktop.addInternalFrame(frame, title, 600, 500);
+   Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
+  void addTreeMenuItem(final TreePanel treePanel, String title)
+  {
+    final JMenuItem item = new JMenuItem(title);
+    sortByTreeMenu.add(item);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addHistoryItem("sort");
+        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+        alignPanel.repaint();
+      }
+    });
+
+    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+      {
+        sortByTreeMenu.remove(item);
+      };
+    });
+
+  }
 
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"
-                                  +"\nwithin the Barton Group, Dundee University."
-                                  +"\nThis will be available as a web service 2005",
-                                  "Web service", JOptionPane.INFORMATION_MESSAGE);
+     WebserviceInfo info = new WebserviceInfo("Clustal web service",
+     "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
+     " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+    +" Nucleic Acids Research, submitted, June 1994.",
+     450, 150);
+
+    ClustalThread thread = new ClustalThread(info);
+    thread.start();
   }
 
-  public void pdbTest_actionPerformed(ActionEvent e)
-  {
-   String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
+    class ClustalThread extends Thread
+    {
+      WebserviceInfo info;
+      public ClustalThread(WebserviceInfo info)
+      {this.info = info; }
 
-   String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
-   if (reply.length()>1)
-     url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
+      public void run()
+      {
+        info.setStatus(WebserviceInfo.STATE_RUNNING);
+        jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
+        Vector sv = viewport.getAlignment().getSequences();
+        SequenceI[] seqs = new SequenceI[sv.size()];
 
-   try
-   {
-     PDBfile pdb = new PDBfile(url,
-                               "URL");
-    Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
-    seq.setPDBfile(pdb);
-     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
-     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
-  // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
-
-     rotCanvas rc = new rotCanvas(pdb);
-     JInternalFrame frame = new JInternalFrame();
-     frame.setContentPane(rc);
-     Desktop.addInternalFrame(frame, url, 400,400);
-   }
-   catch (Exception ex)
-   {
-     ex.printStackTrace();
-   }
+        int i = 0;
+        do
+        {
+          seqs[i] = (SequenceI) sv.elementAt(i);
+        }
+        while (++i < sv.size());
 
-  }
+        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+        if (alignment != null)
+        {
+          AlignFrame af = new AlignFrame(new Alignment(alignment));
+          Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
+                                   NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+          af.clustalColour_actionPerformed(null);
+          af.clustalColour.setSelected(true);
+          info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else
+        {
+            info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+            info.appendProgressText("Problem obtaining clustal alignment");
+        }
+      }
+    }
 
+  protected void jpred_actionPerformed(ActionEvent e)
+{
 
-  public void doKeyPressed(KeyEvent evt)
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
+      }
+      else
+      {
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.elementAt(0));
+      }
+      else
+      {
+        SequenceI[] msa = new SequenceI[seqs.size()];
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+  }
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
   {
+    // TODO:resolve which menu item was actually selected
+    // Now, check we have enough sequences
+      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;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
+      }
+      else
+      {
+        Vector seqs = viewport.getAlignment().getSequences();
 
-    System.out.println(evt.getKeyChar());
-    if(evt.isControlDown() && evt.getKeyChar()=='f')
-      findMenuItem_actionPerformed(null);
+        if (seqs.size() > 1) {
+          SequenceI[] msa = new SequenceI[seqs.size()];
+          for (int i = 0; i < seqs.size(); i++)
+          {
+            msa[i] = (SequenceI) seqs.elementAt(i);
+          }
 
+          MsaWSClient ct = new MsaWSClient(msa);
+        }
+
+      }
+    }
+
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Select a newick-like tree file");
+    chooser.setToolTipText("Load a tree file");
+    int value = chooser.showOpenDialog(null);
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
+        ShowNewickTree(fin, choice);
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
+  }
+
+  public void ShowNewickTree(NewickFile nf, String title)
+  {
+    try{
+      nf.parse();
+      if (nf.getTree() != null)
+      {
+        TreePanel tp = new TreePanel(viewport,
+                                     viewport.getAlignment().getSequences(),
+                                     nf, "FromFile", title);
+        Desktop.addInternalFrame(tp, title, 600, 500);
+        addTreeMenuItem(tp, title);
+        viewport.setCurrentTree(tp.getTree());
+      }
+     }catch(Exception ex){ex.printStackTrace();}
   }