/********************
 * 2004 Jalview Reengineered
 * Barton Group
 * Dundee University
 *
 * AM Waterhouse
 *******************/




package jalview.gui;

import jalview.jbgui.GAlignFrame;
import jalview.schemes.*;
import jalview.datamodel.*;
import jalview.analysis.*;
import jalview.io.*;
import jalview.ws.*;
import MCview.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.print.*;
import javax.swing.*;
import javax.swing.event.*;
import java.util.*;
import jalview.datamodel.SequenceI;

public class AlignFrame extends GAlignFrame
{
  final AlignmentPanel alignPanel;
  final AlignViewport viewport;
  public AlignFrame(AlignmentI al)
  {
    super();

    viewport = new AlignViewport(al,true,true,true,false);
    alignPanel = new AlignmentPanel(this, viewport);
    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
    fontNameMenuItem.setText(viewport.getFont().getName());
    fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
  }

  protected void saveAs_actionPerformed(ActionEvent e)
  {
    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
    chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
    chooser.setToolTipText("Save");
    int value = chooser.showSaveDialog(this);
    if(value == JFileChooser.APPROVE_OPTION)
    {
      String choice =  chooser.getSelectedFile().getPath();
      jalview.bin.Cache.LAST_DIRECTORY = choice;
      String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
      try{
        java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
        out.println(output);
        out.close();
      }
      catch(Exception ex){}
    }

  }

  protected void outputText_actionPerformed(ActionEvent e)
  {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
     JInternalFrame frame = new JInternalFrame();
     cap.formatForOutput();
     frame.setContentPane(cap);
     Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
     cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
  }

  protected void htmlMenuItem_actionPerformed(ActionEvent e)
  {
    HTMLOutput htmlOutput = new HTMLOutput(viewport);
    htmlOutput = null;
  }

  public void printMenuItem_actionPerformed(ActionEvent e)
  {
    //Putting in a thread avoids Swing painting problems
    PrintThread thread = new PrintThread();
    thread.start();
  }

  class PrintThread extends Thread
  {
    public void run()
    {
      PrinterJob printJob = PrinterJob.getPrinterJob();
      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
      printJob.setPrintable(alignPanel, pf);
      if (printJob.printDialog())
      {
        try
        {
          printJob.print();
        }
        catch (Exception PrintException)
        {
          PrintException.printStackTrace();
        }
      }
    }

  }




  public void closeMenuItem_actionPerformed(ActionEvent e)
  {
    try{
      this.setClosed(true);
    }catch(Exception ex){}
  }

  ArrayList  historyList = new ArrayList();
  ArrayList redoList = new ArrayList();

  void updateEditMenuBar()
  {
    if(historyList.size()>0)
     {
       undoMenuItem.setEnabled(true);
       Object [] history = (Object[])historyList.get(0);
       undoMenuItem.setText("Undo "+history[0]);
     }
    else
    {
      undoMenuItem.setEnabled(false);
      undoMenuItem.setText("Undo");
    }

    if(redoList.size()>0)
     {
       redoMenuItem.setEnabled(true);
       Object [] history = (Object[])redoList.get(0);
       redoMenuItem.setText("Redo "+history[0]);
     }
    else
    {
      redoMenuItem.setEnabled(false);
      redoMenuItem.setText("Redo");
    }
  }

  public void addHistoryItem(String type)
  {
    // 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++)
    {
      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
                             viewport.getAlignment().getSequenceAt(i).getSequence());
    }

    historyList.add(0, new Object[]{type,  seq} );
    updateEditMenuBar();
  }

  protected void undoMenuItem_actionPerformed(ActionEvent e)
  {
    Object [] history = (Object[])historyList.remove(0);
    // add the redo state before continuing!!
    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
    {
      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
                            viewport.getAlignment().getSequenceAt(i).
                            getSequence());
    }
    /////////

    redoList.add(0, new Object[] {history[0], seq});

      seq = (SequenceI[]) history[1];
      viewport.setAlignment( new Alignment(seq) );
      updateEditMenuBar();
      alignPanel.RefreshPanels();
  }


  protected void redoMenuItem_actionPerformed(ActionEvent e)
  {
     Object [] history = (Object[])redoList.remove(0);
     SequenceI[] seq = (SequenceI[]) history[1];
     viewport.setAlignment( new Alignment(seq) );
     updateEditMenuBar();
     alignPanel.RefreshPanels();
  }


  public void groupsMenuItem_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);
  }

  protected void deleteGroups_actionPerformed(ActionEvent e)
  {
    viewport.alignment.deleteAllGroups();
    viewport.getSelection().clear();

    alignPanel.RefreshPanels();
  }



  public void selectAllSequenceMenuItem_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);
  }

  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setRubberbandGroup(null);
    viewport.getSelection().clear();
    PaintRefresher.Refresh(null);
  }

  public void invertSequenceMenuItem_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);
  }


  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.getColumnSelection().clear();
    repaint();
  }

  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem("delete columns");
    ColumnSelection colSel = viewport.getColumnSelection();
    if (colSel.size() > 0)
    {
      int min = colSel.getMin();
      viewport.getAlignment().trimLeft(min);
      colSel.compensateForEdit(0,min);
      alignPanel.RefreshPanels();
    }
  }

  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem("delete columns");
    ColumnSelection colSel = viewport.getColumnSelection();
    if (colSel.size() > 0)
    {
      int max = colSel.getMax();
      if(max>1)
        viewport.getAlignment().trimRight(max);

      alignPanel.RefreshPanels();
    }

  }

  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem("delete gapped columns");
    viewport.getAlignment().removeGaps();
    alignPanel.RefreshPanels();
  }

  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem("delete all gaps");
    SequenceI current;
    int jSize;
    for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
    {
      current = viewport.getAlignment().getSequenceAt(i);
      jSize = current.getLength();
      for (int j=0; j < jSize; j++)
        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
        {
          current.deleteCharAt(j);
          j--;
          jSize--;
        }
    }

    alignPanel.RefreshPanels();
  }

  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");
    Finder finder = new Finder(viewport, alignPanel, frame);
    frame.setClosable(true);
    frame.setContentPane(finder);
    frame.setSize(340,110);
    frame.setVisible(true);
  }



  public void fontNameMenuItem_actionPerformed(ActionEvent e)
  {
    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();


    String selection = JOptionPane.showInternalInputDialog(this,
                                "Select font",
                                "Font selection",
                                JOptionPane.QUESTION_MESSAGE,
                                null,fonts
                                ,fontNameMenuItem.getText()).toString();
    if(selection!=null)
    {
       fontNameMenuItem.setText(selection);
       SetFont();
     }

  }

  public void fontSizeMenuItem_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();
     }
  }

  public void fontStyleMenuItem_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();
    }

  }

  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
  {
      viewport.setColourText( colourTextMenuItem.isSelected() );
      alignPanel.RefreshPanels();
  }

  void SetFont()
  {
      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();

  }

  protected void wrapMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
    alignPanel.RefreshPanels();
  }


  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
    alignPanel.RefreshPanels();
  }

  public void viewTextMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setShowText( viewTextMenuItem.isSelected() );
    alignPanel.RefreshPanels();
  }


  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
    alignPanel.RefreshPanels();
  }

  public void secondaryStructure_actionPerformed(ActionEvent evt)
  {
    alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());
  }

  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
  {
    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.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);
     frame.setContentPane(overview);
    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
                             frame.getWidth(), frame.getHeight());
    frame.pack();
    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);
   }


  }

  protected void noColourmenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( null );
    changeColour();
  }


  public void clustalColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
    conservationMenuItem.setSelected(false);
    abovePIDThreshold.setSelected(false);
    changeColour();
  }

  public void zappoColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new ZappoColourScheme() );
    changeColour();
  }

  public void taylorColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new TaylorColourScheme() );
    changeColour();
  }


  public void hydrophobicityColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
    changeColour();
  }

  public void helixColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new HelixColourScheme()  );
    changeColour();
  }


  public void strandColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new StrandColourScheme() );
    changeColour();
  }


  public void turnColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new TurnColourScheme() );
    changeColour();
  }


  public void buriedColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new BuriedColourScheme() );
    changeColour();
  }

  public void nucleotideColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new NucleotideColourScheme() );
    changeColour();
  }


  void changeColour()
  {
    if(abovePIDThreshold.isSelected())
      abovePIDThreshold_actionPerformed(null);
    else if(conservationMenuItem.isSelected())
      conservationMenuItem_actionPerformed(null);


     alignPanel.RefreshPanels();
  }

  void addConservationOrPIDColour()
  {
    int x=0, y=0, threshold = 70;

    if(sliderFrame!=null)
       try
       {
         x = sliderFrame.getX();
         y = sliderFrame.getY();
         SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
         threshold = sp.getValue();
         sliderFrame.setClosed(true);
       }
       catch (Exception ex)
       {    ex.printStackTrace();   }

     ColourSchemeI oldCs = viewport.getGlobalColourScheme();

     ConservationColourScheme ccs = null;
     if (oldCs instanceof ConservationColourScheme)
       ccs = (ConservationColourScheme) oldCs;

     if(conservationMenuItem.isSelected())
     {
       Alignment al = (Alignment)viewport.alignment;
       Conservation c = new Conservation("All",
                            ResidueProperties.propHash, 3, al.getSequences(), 0,
                            al.getWidth() );

       c.calculate();
       c.verdict(false, 100);

       if(ccs!=null)
         ccs = new ConservationColourScheme(c, ccs.cs);
       else
         ccs = new ConservationColourScheme(c, oldCs);

        viewport.setGlobalColourScheme( ccs );

     }
     else if(oldCs instanceof ConservationColourScheme)
     {
       oldCs = ccs.cs;
       viewport.setGlobalColourScheme( oldCs );
     }


     if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
     {
       sliderFrame = new JInternalFrame();
       sliderFrame.setMaximizable(false);
       sliderFrame.setResizable(false);

       SliderPanel sp = null;
       if (conservationMenuItem.isSelected())
       {
        if(threshold > 50)
          threshold = 30;
        sp = new SliderPanel(alignPanel, threshold, true,ccs);
        Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);
        threshold = 0;
       }
       else if (abovePIDThreshold.isSelected())
       {
         sp = new SliderPanel(alignPanel, threshold, false, oldCs);
         sp.cs = oldCs;
         Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
       }

       sliderFrame.setContentPane(sp);
       if(x!=0 && y!=0)
               sliderFrame.setLocation(x,y);

     }
     else
       threshold = 0;


     if (oldCs instanceof ResidueColourScheme)
     {
       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
       rcs.setThreshold(threshold);
     }
     else if (oldCs instanceof ScoreColourScheme)
     {
       ScoreColourScheme scs = (ScoreColourScheme) oldCs;
       scs.setThreshold(threshold);
     }


  }

  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
  {
   if(abovePIDThreshold.isSelected())
    abovePIDThreshold.setSelected(false);

   viewport.setConservationSelected(conservationMenuItem.isSelected());

   addConservationOrPIDColour();
  }

  JInternalFrame sliderFrame;
  public void abovePIDThreshold_actionPerformed(ActionEvent e)
  {
      if(conservationMenuItem.isSelected())
        conservationMenuItem.setSelected(false);

      addConservationOrPIDColour();
  }



  public void userDefinedColour_actionPerformed(ActionEvent e)
  {
    JInternalFrame frame = new JInternalFrame();
    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
    frame.setContentPane(chooser);
    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
    frame.setResizable(false);
    frame.setIconifiable(false);
    frame.setMaximizable(false);
  }

  public void PIDColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new PIDColourScheme() );
    alignPanel.setColourScheme( );
  }


  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
    alignPanel.setColourScheme();
  }



  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
  {
    ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
    Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
  }


  public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem("sort");
    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
    alignPanel.RefreshPanels();
  }

  public void sortIDMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem("sort");
    AlignmentSorter.sortByID( viewport.getAlignment() );
    alignPanel.RefreshPanels();
  }

  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
  {
    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();
  }

  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);
    frame.setMaximizable(false);
    frame.setResizable(false);

  }

  public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
  {
    if(viewport.getSelection().size()<2)
      JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
    else
    {
      JInternalFrame frame = new JInternalFrame();
      frame.setContentPane(new PairwiseAlignPanel(viewport));
      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
    }
  }

  public void PCAMenuItem_actionPerformed(ActionEvent e)
  {
    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
       || viewport.getAlignment().getHeight()<4)
    {
      JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
                                    +"at least 4 input sequences.",
                                    "Sequence selection insufficient",
                                    JOptionPane.WARNING_MESSAGE);
      return;
    }

    try{
      PCAPanel pcaPanel = new PCAPanel(viewport, null);
      JInternalFrame frame = new JInternalFrame();
      frame.setContentPane(pcaPanel);
      Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
   }catch(java.lang.OutOfMemoryError ex)
   {
     JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
   }


  }

  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("AV", "PID", "Average distance tree using PID");
  }

  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
  }


  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
  }

  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
  }

  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());
   }

   frame.setContentPane(tp);
   Desktop.addInternalFrame(frame, title, 600, 500);
  }




  public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
  {
    JInternalFrame frame = new JInternalFrame();
    ClustalThread ct = new ClustalThread(frame);
    Thread t = new Thread(ct);
    t.start();
    frame.setContentPane(ct);
     Desktop.addInternalFrame(frame, title, 300, 80);

  }

  class ClustalThread extends JPanel implements Runnable
  {
    Image [] image;
    int imageIndex = 0;
    boolean webServiceRunning = false;
    JInternalFrame frame;
    public ClustalThread(JInternalFrame frame)
    {
      this.frame = frame;
      image = new Image[9];
      for(int i=0; i<9; i++)
      {
        java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
        if (url != null)
        {
          image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
          MediaTracker mt = new MediaTracker(this);
          mt.addImage(image[i], i);
          try{mt.waitForID(i);}
          catch(Exception ex){}
        }
      }
      DNATwirler twirler = new DNATwirler();
      twirler.start();
      webServiceRunning = true;
    }

    class DNATwirler extends Thread
    {
      public void run()
      {
        while(webServiceRunning)
        {
          try{
            Thread.sleep(100);
            imageIndex++;
            imageIndex %=9;
            repaint();
          }
          catch(Exception ex){}
        }
      }
    }

    // JBPNote
    // Should check to see if the server settings are valid
    // Need visual-delay indication here.
    public void run()
       {
         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
         Vector sv = viewport.getAlignment().getSequences();
         SequenceI[] seqs = new SequenceI[sv.size()];

         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, getTitle().concat(" - ClustalW Alignment"),
                                    700, 500); // JBPNote - is there a new window geom. property ?
         }
         else
           JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
                                         JOptionPane.WARNING_MESSAGE);

         webServiceRunning = false;
         try{
           frame.setClosed(true);
         }catch(Exception ex){}
       }

       public void paintComponent(Graphics g)
       {
         g.setColor(Color.white);
         g.fillRect(0,0,getWidth(), getHeight());
         if(image!=null)
         {
           g.drawImage(image[imageIndex],10,10,this);
         }
         g.setFont(new Font("Arial", Font.BOLD, 12));
         g.setColor(Color.black);
         g.drawString("Clustal Alignment Web Service running", 30,30);
       }


  }


  public void pdbTest_actionPerformed(ActionEvent e)
  {
   String reply =
       JOptionPane.showInternalInputDialog(this, "Enter pdb code",
                                           "PDB test viewer", JOptionPane.QUESTION_MESSAGE);

   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;

   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();
   }

  }


  public void doKeyPressed(KeyEvent evt)
  {

    System.out.println(evt.getKeyChar());
    if(evt.isControlDown() && evt.getKeyChar()=='f')
      findMenuItem_actionPerformed(null);

  }


}