/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/

package jalview.gui;

import java.util.*;

import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.event.*;
import java.awt.print.*;
import javax.swing.*;
import javax.swing.event.*;

import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.ws.*;
import java.beans.PropertyChangeEvent;

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)
  {
    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);

    addInternalFrameListener(new InternalFrameAdapter()
   {
     public void internalFrameActivated(InternalFrameEvent evt)
     {
          javax.swing.SwingUtilities.invokeLater(new Runnable()
          {
            public void run()
            {      alignPanel.requestFocus();    }
          });

     }
   });

  }

  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
  {
    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 == JalviewFileChooser.APPROVE_OPTION)
    {
      currentFileFormat  = chooser.getSelectedFormat();
      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat);

      if (currentFileFormat.equals("Jalview"))
      {
        String shortName = title;
        if(shortName.indexOf(java.io.File.separatorChar)>-1)
              shortName = shortName.substring(
                    shortName.lastIndexOf(java.io.File.separatorChar)+1);

        String choice = chooser.getSelectedFile().getPath();
        Jalview2XML.SaveState(this, choice, shortName);
        // USE Jalview2XML to save this file
        return;
      }

      String choice =  chooser.getSelectedFile().getPath();
      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);
        out.close();
      }
      catch(Exception ex){}
    }

  }

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

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

  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
    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){}
  }

  Stack historyList = new Stack();
  Stack redoList = new Stack();
  private int treeCount = 0;

  void updateEditMenuBar()
   {
     if(historyList.size()>0)
      {
        undoMenuItem.setEnabled(true);
        HistoryItem hi = (HistoryItem)historyList.peek();
        undoMenuItem.setText("Undo "+hi.getDescription());
      }
     else
     {
       undoMenuItem.setEnabled(false);
       undoMenuItem.setText("Undo");
     }

     if(redoList.size()>0)
      {
        redoMenuItem.setEnabled(true);
        HistoryItem hi = (HistoryItem)redoList.peek();
        redoMenuItem.setText("Redo "+hi.getDescription());
      }
     else
     {
       redoMenuItem.setEnabled(false);
       redoMenuItem.setText("Redo");
     }
   }

   public void addHistoryItem(HistoryItem hi)
   {
     historyList.push(hi);
     updateEditMenuBar();
   }

   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
       HistoryItem hi = (HistoryItem)historyList.pop();
       redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
       restoreHistoryItem(hi);
   }


   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
      HistoryItem hi = (HistoryItem)redoList.pop();
      restoreHistoryItem(hi);
      updateEditMenuBar();
      viewport.updateConsensus();
      alignPanel.repaint();
      alignPanel.repaint();
   }


   // used by undo and redo
   void restoreHistoryItem(HistoryItem hi)
   {
      if(hi.getType()== HistoryItem.SORT)
      {
           for(int i=0; i<hi.getSequences().size(); i++)
             viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
      }
      else
      {
        for (int i = 0; i < hi.getSequences().size(); i++)
        {
          SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
          if(restore.getLength()==0)
          {
            restore.setSequence(hi.getHidden().elementAt(i).toString());
            viewport.alignment.getSequences().insertElementAt(
               restore,
               hi.getAlignIndex(i));
          }
          else
            restore.setSequence(hi.getHidden().elementAt(i).toString());
        }
        if(hi.getType()==HistoryItem.PASTE)
        {
          for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
            viewport.alignment.deleteSequence(i);
        }
      }
      updateEditMenuBar();

      viewport.updateConsensus();
      viewport.updateConservation();
      alignPanel.repaint();
      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
  }

  public void moveSelectedSequences(boolean up)
  {
    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();
  }



  protected void copy_actionPerformed(ActionEvent e)
  {
     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 ) ;

  }


  protected void pasteNew_actionPerformed(ActionEvent e)
  {
    paste(true);
  }

  protected void pasteThis_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
    paste(false);
  }

  void paste(boolean newAlignment)
  {
    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.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
        viewport.setEndSeq(viewport.alignment.getHeight());
        viewport.alignment.getWidth();
        viewport.updateConservation();
        viewport.updateConsensus();
        alignPanel.repaint();
      }

    }catch(Exception ex){}// could be anything being pasted in here

  }


  protected void cut_actionPerformed(ActionEvent e)
  {
    copy_actionPerformed(null);
    delete_actionPerformed(null);
  }

  protected void delete_actionPerformed(ActionEvent e)
  {
    boolean seqsdeleted=false;

    if (viewport.getSelectionGroup() == null)
      return;

    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));

     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) {
         seqsdeleted=true;
         viewport.getAlignment().deleteSequence(seq);
        } else {
         viewport.getAlignment().getSequences().setElementAt(seq, index);
       }
     }

     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
     if (seqsdeleted)
       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
     if(viewport.getAlignment().getHeight()<1)
     try
     {
       this.setClosed(true);
     }catch(Exception ex){}
   viewport.updateConservation();
   viewport.updateConsensus();
   alignPanel.repaint();
 }


  protected void deleteGroups_actionPerformed(ActionEvent e)
  {
    viewport.alignment.deleteAllGroups();
    viewport.setSelectionGroup(null);
    alignPanel.repaint();
  }



  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 deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setSelectionGroup(null);
    viewport.getColumnSelection().clear();
    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)
  {
    ColumnSelection colSel = viewport.getColumnSelection();
    if (colSel.size() > 0)
    {
      addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
                                     HistoryItem.HIDE));
      int min = colSel.getMin();
      viewport.getAlignment().trimLeft(min);
      colSel.compensateForEdit(0,min);

      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();
    }
  }

  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
  {
    ColumnSelection colSel = viewport.getColumnSelection();
    if (colSel.size() > 0)
    {
      addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
                                     HistoryItem.HIDE));

      int max = colSel.getMax();
      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.repaint();
    }

  }

  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                   viewport.alignment,
                                   HistoryItem.HIDE));

    viewport.getAlignment().removeGaps();
    viewport.updateConservation();
    viewport.updateConsensus();
    alignPanel.repaint();
  }

  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Remove Gaps",
                                   viewport.alignment,
                                   HistoryItem.HIDE));
    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--;
        }
    }
    viewport.updateConservation();
    viewport.updateConsensus();
    alignPanel.repaint();
  }


  public void padGapsMenuitem_actionPerformed(ActionEvent e)
    {
      addHistoryItem(new HistoryItem("Pad Gaps",
                                     viewport.alignment,
                                     HistoryItem.HIDE));
      SequenceI current;
      int Width = viewport.getAlignment().getWidth()-1;
      for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
      {
        current = viewport.getAlignment().getSequenceAt(i);

        if (current.getLength()<Width)
          current.insertCharAt(Width, viewport.getGapCharacter());
      }
      viewport.updateConservation();
      viewport.updateConsensus();
      alignPanel.repaint();
  }


  public void findMenuItem_actionPerformed(ActionEvent e)
  {
    JInternalFrame frame = new JInternalFrame();
    Finder finder = new Finder(viewport, alignPanel, frame);
    frame.setContentPane(finder);
    Desktop.addInternalFrame(frame, "Find", 340,110);
    frame.setLayer(JLayeredPane.PALETTE_LAYER);

  }


  public void font_actionPerformed(ActionEvent e)
  {
    FontChooser fc = new FontChooser( alignPanel );
  }

  protected void fullSeqId_actionPerformed(ActionEvent e)
  {
    viewport.setShowFullId( fullSeqId.isSelected() );

    alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
    alignPanel.repaint();
  }

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

  protected void wrapMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
    scaleAbove.setVisible( wrapMenuItem.isSelected() );
    scaleLeft.setVisible( wrapMenuItem.isSelected() );
    scaleRight.setVisible( wrapMenuItem.isSelected() );
    alignPanel.repaint();
  }

  protected void scaleAbove_actionPerformed(ActionEvent e)
  {
    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
    alignPanel.repaint();
  }

  protected void scaleLeft_actionPerformed(ActionEvent e)
  {
    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
    alignPanel.repaint();
  }

  protected void scaleRight_actionPerformed(ActionEvent e)
  {
    viewport.setScaleRightWrapped(scaleRight.isSelected());
    alignPanel.repaint();
  }



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

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


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

  public void sequenceFeatures_actionPerformed(ActionEvent evt)
  {
    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 annotationPanelMenuItem_actionPerformed(ActionEvent e)
  {
    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 = 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 );


  }

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


  public void clustalColour_actionPerformed(ActionEvent e)
  {
    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
  }

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

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


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

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


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


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


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

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


  protected void applyToAllGroups_actionPerformed(ActionEvent e)
  {
    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
  }



  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);

      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
      ccs.setConsensus( viewport.vconsensus );
      viewport.setGlobalColourScheme(ccs);

      ccs.inc = 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==null)
          sg.cs = null;
        else if (cs instanceof ClustalxColourScheme)
          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
        else if (cs instanceof UserColourScheme)
          sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
        else
          try{
            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
          }catch(Exception ex){}

        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)
  {
      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();
    }
  }


  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
  {
    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 abovePIDThreshold_actionPerformed(ActionEvent e)
  {
    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 userDefinedColour_actionPerformed(ActionEvent e)
  {
    new UserDefinedColours( alignPanel, null);
  }

  public void PIDColour_actionPerformed(ActionEvent e)
  {
    changeColour( new PIDColourScheme() );
  }


  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
  {
    changeColour(new Blosum62ColourScheme() );
  }



  public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
    alignPanel.repaint();
  }

  public void sortIDMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
    AlignmentSorter.sortByID( viewport.getAlignment() );
    alignPanel.repaint();
  }

  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
  //  AlignmentSorter.sortByGroup(viewport.getAlignment());
    AlignmentSorter.sortGroups(viewport.getAlignment());
    alignPanel.repaint();
  }

  public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
  {
    RedundancyPanel sp = new RedundancyPanel(alignPanel,this);
    JInternalFrame frame = new JInternalFrame();
    frame.setContentPane(sp);
    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);

  }

  public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
  {
    if((viewport.getSelectionGroup()==null) ||
       viewport.getSelectionGroup().getSize()<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.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>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 BLOSUM62");
  }

  void NewTreePanel(String type, String pwType, String title)
  {
    String ltitle;
    final TreePanel tp;
    if (viewport.getSelectionGroup() != null &&
        viewport.getSelectionGroup().getSize() > 3)
    {
      int s=0;
      SequenceGroup sg = viewport.getSelectionGroup();

      /* Decide if the selection is a column region */
      while (s<sg.sequences.size()) {
        if (((SequenceI) sg.sequences.elementAt(s++)).getLength()<sg.getEndRes()) {
          JOptionPane.showMessageDialog(Desktop.desktop,
                                        "The selected region to create a tree may\nonly contain residues or gaps.\n"
                                       +"Try using the Pad function in the edit menu,\n"
                                      +"or one of the multiple sequence alignment web services.",
                                        "Sequences in selection are not aligned", JOptionPane.WARNING_MESSAGE);
          return;
        }

      }
      title=title+" on region";
      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
                         pwType,
                         sg.getStartRes(), sg.getEndRes());
    }
    else
    {

     //are the sequences aligned?
     if(!viewport.alignment.isAligned())
     {
       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
                                     +"Try using the Pad function in the edit menu,\n"
                                     +"or one of the multiple sequence alignment web services.",
                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
       return;
     }
     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
                        type, pwType, 0, viewport.alignment.getWidth());
   }

   addTreeMenuItem(tp, title);
   viewport.setCurrentTree(tp.getTree());

   Desktop.addInternalFrame(tp, title+" from "+this.title, 600, 500);
  }

  public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
    final JMenuItem item = new JMenuItem("by "+title);
    sort.add(item);
    item.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
                                       HistoryItem.SORT));
        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
        AlignmentSorter.sortBy(viewport.getAlignment(), order);
        alignPanel.repaint();
      }
    });
  }

  void addTreeMenuItem(final TreePanel treePanel, String title)
  {
    final JMenuItem item = new JMenuItem(title);

    treeCount++;

    if (treeCount==1)
      sort.add(sortByTreeMenu);

    sortByTreeMenu.add(item);
    item.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
                                       HistoryItem.SORT));
        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
        alignPanel.repaint();
      }
    });

    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
    {
      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
      {
        treeCount--;
        sortByTreeMenu.remove(item);
        if (treeCount==0)
          sort.remove(sortByTreeMenu);
      };
    });
    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() {
      public void propertyChange(PropertyChangeEvent evt)
      {
        if (evt.getPropertyName().equals("alignment")) {
          treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
          treePanel.repaint();
        }
      }

    }
    );
  }


  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)
  {
      // 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, true, true);
        }
  }


  protected void jpred_actionPerformed(ActionEvent e)
{
    SequenceI seq=null;
    SequenceI[] msa=null;

    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())
      {
        seq = (SequenceI)seqs.getSequenceAt(0);
      }
      else
      {
        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 || !viewport.alignment.isAligned())
      {
        seq = (SequenceI) seqs.elementAt(0);
      }
      else
      {
        msa = new SequenceI[seqs.size()];
        for (int i = 0; i < seqs.size(); i++)
        {
          msa[i] = (SequenceI) seqs.elementAt(i);
        }
      }
    }
    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);
        }


      }
      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) {
        MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, false, true);
      }
  }
    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();}
  }

}