/*
 * 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 Softwarechang
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.gui;

import java.beans.*;
import java.io.*;
import java.util.*;

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

import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.ws.*;
import javax.swing.event.AncestorEvent;

/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class AlignFrame
    extends GAlignFrame implements ClipboardOwner
{
  /** DOCUMENT ME!! */
  public static final int NEW_WINDOW_WIDTH = 700;

  /** DOCUMENT ME!! */
  public static final int NEW_WINDOW_HEIGHT = 500;
  AlignmentPanel alignPanel;
  AlignViewport viewport;

  Vector viewports = new Vector();
  Vector alignPanels = new Vector();

  /** DOCUMENT ME!! */
  public String currentFileFormat = null;
  Stack historyList = new Stack();
  Stack redoList = new Stack();
  private int treeCount = 0;


  /**
   * Creates a new AlignFrame object.
   *
   * @param al DOCUMENT ME!
   */
  public AlignFrame(AlignmentI al)
  {
    viewport = new AlignViewport(al);
    viewports.add(viewport);


    if(viewport.vconsensus==null)
    {
      //Out of memory calculating consensus.
      BLOSUM62Colour.setEnabled(false);
      PIDColour.setEnabled(false);
      conservationMenuItem.setEnabled(false);
      modifyConservation.setEnabled(false);
      abovePIDThreshold.setEnabled(false);
      modifyPID.setEnabled(false);
    }

    alignPanel = new AlignmentPanel(this, viewport);
    alignPanels.add(alignPanel);

    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");

    if(sortby.equals("Id"))
      sortIDMenuItem_actionPerformed(null);
    else if(sortby.equals("Pairwise Identity"))
      sortPairwiseMenuItem_actionPerformed(null);

   // remove(tabbedPane);
    getContentPane().add(alignPanel, BorderLayout.CENTER);



  //  tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);

    ///Dataset tab
    /////////////////////////
    if(al.getDataset()==null)
    {
      al.setDataset(null);
    }
   // AlignViewport ds = new AlignViewport(al.getDataset(), true);
   // AlignmentPanel dap = new AlignmentPanel(this, ds);
  //  tabbedPane.add("Dataset", dap);
  //  viewports.add(ds);
  //  alignPanels.add(dap);
    /////////////////////////


    viewport.addPropertyChangeListener(new PropertyChangeListener()
    {
     public void propertyChange(PropertyChangeEvent evt)
     {
       if (evt.getPropertyName().equals("alignment"))
       {
         alignmentChanged();
       }
     }
   });


  if (Desktop.desktop != null)
  {
    addServiceListeners();
    setGUINucleotide(al.isNucleotide());
  }
  }

  /* Set up intrinsic listeners for dynamically generated GUI bits. */
  private void addServiceListeners()
  {
    final java.beans.PropertyChangeListener thisListener;
    // Do this once to get current state
    BuildWebServiceMenu();
    Desktop.discoverer.addPropertyChangeListener(
        thisListener = new java.beans.PropertyChangeListener()
    {
      public void propertyChange(PropertyChangeEvent evt)
      {
        // System.out.println("Discoverer property change.");
        if (evt.getPropertyName().equals("services"))
        {
          // System.out.println("Rebuilding web service menu");
          BuildWebServiceMenu();
        }
      }
    });
    addInternalFrameListener(new javax.swing.event.
                             InternalFrameAdapter()
    {
      public void internalFrameClosed(
          javax.swing.event.InternalFrameEvent evt)
      {
        // System.out.println("deregistering discoverer listener");
        Desktop.discoverer.removePropertyChangeListener(thisListener);
        closeMenuItem_actionPerformed(null);
      }
      ;
    });

  }

  public void setGUINucleotide(boolean nucleotide)
  {
    showTranslation.setVisible( nucleotide );
    sequenceFeatures.setVisible(!nucleotide );
    featureSettings.setVisible( !nucleotide );
    conservationMenuItem.setVisible( !nucleotide );
    modifyConservation.setVisible(   !nucleotide );

    //Deal with separators
    //Remember AlignFrame always starts as protein
    if(nucleotide)
    {
      viewMenu.remove(viewMenu.getItemCount()-2);
    }
    else
    {
      calculateMenu.remove(calculateMenu.getItemCount()-2);
    }
  }


  /*
   Added so Castor Mapping file can obtain Jalview Version
  */
  public String getVersion()
  {
    return  jalview.bin.Cache.getProperty("VERSION");
  }


  /**
   * DOCUMENT ME!
   *
   * @param String DOCUMENT ME!
   */

  public void parseGroupsFile(String file)
  {
    try
    {
      BufferedReader in = new BufferedReader(new FileReader(file));
      SequenceI seq = null;
      String line, type, desc, token;

      int index, start, end;
      StringTokenizer st;
      SequenceFeature sf;
      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
      int lineNo = 0;
      while ( (line = in.readLine()) != null)
      {
        lineNo++;
        st = new StringTokenizer(line, "\t");
        if (st.countTokens() == 2)
        {
          type = st.nextToken();
          UserColourScheme ucs = new UserColourScheme(st.nextToken());
          fr.setColour(type, ucs.findColour("A"));
          continue;
        }

        while (st.hasMoreElements())
        {
          desc = st.nextToken();
          token = st.nextToken();
          if (!token.equals("ID_NOT_SPECIFIED"))
          {
            index = viewport.alignment.findIndex(viewport.alignment.findName(
                token));
            st.nextToken();
          }
          else
          {
            index = Integer.parseInt(st.nextToken());
          }

          start = Integer.parseInt(st.nextToken());
          end = Integer.parseInt(st.nextToken());

          seq = viewport.alignment.getSequenceAt(index);
          start = seq.findIndex(start) - 1;
          end = seq.findIndex(end) - 1;

          type = st.nextToken();

          if (fr.getColour(type) == null)
          {
            // Probably the old style groups file
            UserColourScheme ucs = new UserColourScheme(type);
            fr.setColour(type, ucs.findColour("A"));
          }


          sf = new SequenceFeature(type, desc, "", start, end);

          seq.addSequenceFeature(sf);


         // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
         // sg.addSequence(seq, false);

         // viewport.alignment.addGroup(sg);

        }
      }

      viewport.showSequenceFeatures = true;

      alignPanel.repaint();

    }
    catch (Exception ex)
    {
      System.out.println("Error parsing groups file: " + ex);
    }
  }

  public void fetchSequence_actionPerformed(ActionEvent e)
  {
    new SequenceFetcher(this);
  }


  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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();

        if (currentFileFormat == null)
        {
          JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                                "You must select a file format before saving!",
                                                "File format not specified",
                                                JOptionPane.WARNING_MESSAGE);
          value = chooser.showSaveDialog(this);
          return;
        }

      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                    currentFileFormat);

      String choice = chooser.getSelectedFile().getPath();
      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);

      saveAlignment(choice, currentFileFormat);
    }
  }

  public boolean saveAlignment(String file, String format)
  {
    if (format.equalsIgnoreCase("Jalview"))
    {
      String shortName = title;

      if (shortName.indexOf(java.io.File.separatorChar) > -1)
      {
        shortName = shortName.substring(shortName.lastIndexOf(
            java.io.File.separatorChar) + 1);
      }

      Jalview2XML.SaveAlignment(this, file, shortName);

      // USE Jalview2XML to save this file
      return true;
    }
    else
    {
      String output = new FormatAdapter().formatSequences(format,
          viewport.getAlignment().
          getSequences());
      if (output == null)
      {
        return false;
      }

      try
      {
        java.io.PrintWriter out = new java.io.PrintWriter(
            new java.io.FileWriter(file));

        out.print(output);
        out.close();
        return true;
      }
      catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }
    return false;
  }

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

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void htmlMenuItem_actionPerformed(ActionEvent e)
  {
    new HTMLOutput(viewport,
                   alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
  }

  public void createImageMap(File file, String image)
  {
    alignPanel.makePNGImageMap(file, image);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void createPNG(File f)
  {
    alignPanel.makePNG(f);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void createEPS(File f)
  {
    alignPanel.makeEPS(f);
  }

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

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void closeMenuItem_actionPerformed(ActionEvent e)
  {
    try
    {
      PaintRefresher.components.remove(viewport.alignment);
      this.setClosed(true);
    }
    catch (Exception ex)
    {
    }
  }

  /**
   * DOCUMENT ME!
   */
  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");
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param hi DOCUMENT ME!
   */
  public void addHistoryItem(HistoryItem hi)
  {
    historyList.push(hi);
    updateEditMenuBar();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void undoMenuItem_actionPerformed(ActionEvent e)
  {
    HistoryItem hi = (HistoryItem) historyList.pop();
    redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                  HistoryItem.HIDE));
    restoreHistoryItem(hi);
    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void redoMenuItem_actionPerformed(ActionEvent e)
  {
    HistoryItem hi = (HistoryItem) redoList.pop();
    restoreHistoryItem(hi);
    updateEditMenuBar();
    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
  }

  // 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.firePropertyChange("alignment", null,
                                viewport.getAlignment().getSequences());
  }

  /**
   * DOCUMENT ME!
   *
   * @param up DOCUMENT ME!
   */
  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();
  }

  public void lostOwnership(Clipboard clipboard, Transferable contents)
  {
    Desktop.jalviewClipboard = null;
  }


  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void copy_actionPerformed(ActionEvent e)
  {
    if (viewport.getSelectionGroup() == null)
    {
      return;
    }

    SequenceGroup sg = viewport.getSelectionGroup();

    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();

    Hashtable orderedSeqs = new Hashtable();
    SequenceI[] seqs = new SequenceI[sg.getSize()];

    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, startRes, endRes;
    char ch;

    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++;
        }
      }

      //FIND START RES
      //Returns residue following index if gap
      startRes = seq.findPosition(sg.getStartRes());

      //FIND END RES
      //Need to find the residue preceeding index if gap
      endRes = 0;

      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
      {
        ch = seq.getCharAt(j);
        if (!jalview.util.Comparison.isGap( (ch)))
        {
          endRes++;
        }
      }

      if (endRes > 0)
      {
        endRes += seq.getStart() - 1;
      }

      seqs[i] = new Sequence(seq.getName(),
                             seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
                             startRes,
                             endRes);
      seqs[i].setDescription(seq.getDescription());
      seqs[i].setDBRef(seq.getDBRef());
      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
      seqs[i].setDatasetSequence(seq.getDatasetSequence());

    }

    FastaFile ff = new FastaFile();
    ff.addJVSuffix( viewport.showJVSuffix );
    c.setContents(new StringSelection( ff.print(seqs)), this);
    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void pasteNew_actionPerformed(ActionEvent e)
  {
    paste(true);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void pasteThis_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
                                   HistoryItem.PASTE));
    paste(false);
  }

  /**
   * DOCUMENT ME!
   *
   * @param newAlignment DOCUMENT ME!
   */
  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);
      if(str.length()<1)
        return;

      String format = IdentifyFile.Identify(str, "Paste");
      SequenceI[] sequences;

     if(Desktop.jalviewClipboard!=null)
     {
       // The clipboard was filled from within Jalview, we must use the sequences
       // And dataset from the copied alignment
       sequences = (SequenceI[])Desktop.jalviewClipboard[0];
     }
     else
     {
       sequences = new FormatAdapter().readFile(str, "Paste", format);
     }

      if (newAlignment)
      {

        Alignment alignment = new Alignment(sequences);

        if(Desktop.jalviewClipboard!=null)
           alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
        else
           alignment.setDataset( null );


        AlignFrame af = new AlignFrame(alignment);
        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
      {
        //!newAlignment
        for (int i = 0; i < sequences.length; i++)
        {
          Sequence newseq = new Sequence(sequences[i].getName(),
              sequences[i].getSequence(), sequences[i].getStart(),
              sequences[i].getEnd());
          viewport.alignment.addSequence(newseq);
          if(sequences[i].getDatasetSequence()==null)
          {
             ////////////////////////////
            //Datset needs extension;
            /////////////////////////////
            Sequence ds = new Sequence(sequences[i].getName(),
                                       AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
                                       sequences[i].getStart(),
                                       sequences[i].getEnd());
            newseq.setDatasetSequence(ds);
            viewport.alignment.getDataset().addSequence(ds);
          }

        }
        viewport.setEndSeq(viewport.alignment.getHeight());
        viewport.alignment.getWidth();
        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
      }
    }
    catch (Exception ex)
    {
        // could be anything being pasted in here
    }


  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void cut_actionPerformed(ActionEvent e)
  {
    copy_actionPerformed(null);
    delete_actionPerformed(null);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void delete_actionPerformed(ActionEvent e)
  {

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

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

    SequenceGroup sg = viewport.getSelectionGroup();
    boolean allSequences = false;
    if (sg.sequences.size() == viewport.alignment.getHeight())
    {
      allSequences = true;
    }

    for (int i = 0; i < sg.sequences.size(); i++)
    {
      SequenceI seq = sg.getSequenceAt(i);
      int index = viewport.getAlignment().findIndex(seq);
      seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);

      // If the cut affects all sequences, remove highlighted columns
      if (allSequences)
      {
        viewport.getColumnSelection().removeElements(sg.getStartRes(),
            sg.getEndRes() + 1);
      }

      if (seq.getSequence().length() < 1)
      {
        viewport.getAlignment().deleteSequence(seq);
      }
      else
      {
        viewport.getAlignment().getSequences().setElementAt(seq, index);
      }
    }

    viewport.setSelectionGroup(null);
    viewport.alignment.deleteGroup(sg);

    viewport.firePropertyChange("alignment", null,
                                  viewport.getAlignment().getSequences());



    if (viewport.getAlignment().getHeight() < 1)
    {
      try
      {
        this.setClosed(true);
      }
      catch (Exception ex)
      {
      }
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void deleteGroups_actionPerformed(ActionEvent e)
  {
    viewport.alignment.deleteAllGroups();
    viewport.setSelectionGroup(null);
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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), false);
    }

    sg.setEndRes(viewport.alignment.getWidth() - 1);
    viewport.setSelectionGroup(sg);
    PaintRefresher.Refresh(null, viewport.alignment);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setSelectionGroup(null);
    viewport.getColumnSelection().clear();
    viewport.setSelectionGroup(null);
    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
    alignPanel.annotationPanel.activeRes = null;
    PaintRefresher.Refresh(null, viewport.alignment);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = viewport.getSelectionGroup();

    if (sg == null)
    {
      selectAllSequenceMenuItem_actionPerformed(null);

      return;
    }

    for (int i = 0; i < viewport.getAlignment().getSequences().size();
         i++)
    {
      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
    }

    PaintRefresher.Refresh(null, viewport.alignment);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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);
        }
      }

      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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);
        }
      }

      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                   viewport.alignment, HistoryItem.HIDE));

    //This is to maintain viewport position on first residue
    //of first sequence
    SequenceI seq = viewport.alignment.getSequenceAt(0);
    int startRes = seq.findPosition(viewport.startRes);

    viewport.getAlignment().removeGaps();

    viewport.setStartRes(seq.findIndex(startRes)-1);

   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                   HistoryItem.HIDE));

    //This is to maintain viewport position on first residue
    //of first sequence
    SequenceI seq = viewport.alignment.getSequenceAt(0);
    int startRes = seq.findPosition(viewport.startRes);


    SequenceI current;
    int jSize;

    Vector seqs = null;

    int start = 0;
    int end = viewport.alignment.getWidth();

    if (viewport.getSelectionGroup() != null
        && viewport.getSelectionGroup().sequences != null
        && viewport.getSelectionGroup().sequences.size() > 0)
    {
      seqs = viewport.getSelectionGroup().sequences;
      start = viewport.getSelectionGroup().getStartRes();
      end = viewport.getSelectionGroup().getEndRes()+1;
    }
    else
    {
      seqs = viewport.alignment.getSequences();
    }

    for (int i = 0; i < seqs.size(); i++)
    {
      current = (SequenceI) seqs.elementAt(i);
      jSize = current.getLength();

      // Removing a range is much quicker than removing gaps
      // one by one for long sequences
      int j = start;
      int rangeStart=-1, rangeEnd=-1;

      do
      {
        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
        {
          if(rangeStart==-1)
           {
             rangeStart = j;
             rangeEnd = j+1;
           }
           else
           {
             rangeEnd++;
           }
           j++;
        }
        else
        {
          if(rangeStart>-1)
          {
            current.deleteChars(rangeStart, rangeEnd);
            j-=rangeEnd-rangeStart;
            jSize-=rangeEnd-rangeStart;
            rangeStart = -1;
            rangeEnd = -1;
          }
          else
            j++;
        }
      }
      while (j < end && j < jSize);
      if(rangeStart>-1)
      {
       current.deleteChars(rangeStart, rangeEnd);
      }
    }

    viewport.setStartRes(seq.findIndex(startRes)-1);

    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
  }

 public void alignmentChanged()
 {
   if(viewport.vconsensus!=null)
   {
     viewport.updateConsensus();
     viewport.updateConservation();
   }
   resetAllColourSchemes();
   if(alignPanel.overviewPanel!=null)
     alignPanel.overviewPanel.updateOverviewImage();

   alignPanel.repaint();
 }

  void resetAllColourSchemes()
  {
    ColourSchemeI cs = viewport.globalColourScheme;
    if(cs!=null)
    {
      if (cs instanceof ClustalxColourScheme)
      {
        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
            resetClustalX(viewport.alignment.getSequences(),
                          viewport.alignment.getWidth());
      }

      cs.setConsensus(viewport.vconsensus);
      if (cs.conservationApplied())
      {
        Alignment al = (Alignment) viewport.alignment;
        Conservation c = new Conservation("All",
                                          ResidueProperties.propHash, 3,
                                          al.getSequences(), 0,
                                          al.getWidth() - 1);
        c.calculate();
        c.verdict(false, viewport.ConsPercGaps);

        cs.setConservation(c);
      }
    }

    int s, sSize = viewport.alignment.getGroups().size();
    for(s=0; s<sSize; s++)
    {
      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
      {
        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
      }
      sg.recalcConservation();
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void padGapsMenuitem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                   HistoryItem.HIDE));

    SequenceI current;
    int Width = viewport.getAlignment().getWidth();

    for (int i = 0; i < viewport.getAlignment().getSequences().size();
         i++)
    {
      current = viewport.getAlignment().getSequenceAt(i);

      if (current.getLength() < Width)
      {
        current.insertCharAt(Width - 1, viewport.getGapCharacter());
      }
    }

    alignmentChanged();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void font_actionPerformed(ActionEvent e)
  {
    new FontChooser(alignPanel);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void seqLimit_actionPerformed(ActionEvent e)
  {
    viewport.setShowJVSuffix(seqLimits.isSelected());

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


  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setColourText(colourTextMenuItem.isSelected());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void wrapMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setWrapAlignment(wrapMenuItem.isSelected());
    alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
    scaleAbove.setVisible(wrapMenuItem.isSelected());
    scaleLeft.setVisible(wrapMenuItem.isSelected());
    scaleRight.setVisible(wrapMenuItem.isSelected());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void scaleAbove_actionPerformed(ActionEvent e)
  {
    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void scaleLeft_actionPerformed(ActionEvent e)
  {
    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void scaleRight_actionPerformed(ActionEvent e)
  {
    viewport.setScaleRightWrapped(scaleRight.isSelected());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void viewTextMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setShowText(viewTextMenuItem.isSelected());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param evt DOCUMENT ME!
   */
  public void sequenceFeatures_actionPerformed(ActionEvent evt)
  {
    viewport.showSequenceFeatures(sequenceFeatures.isSelected());

    if (viewport.showSequenceFeatures)
    {
      new SequenceFeatureFetcher(viewport.
         alignment,
          alignPanel);
    }

    featureSettings.setEnabled(true);

    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
    alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void noColourmenuItem_actionPerformed(ActionEvent e)
  {
    changeColour(null);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void clustalColour_actionPerformed(ActionEvent e)
  {
    changeColour(new ClustalxColourScheme(
        viewport.alignment.getSequences(), viewport.alignment.getWidth()));
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void zappoColour_actionPerformed(ActionEvent e)
  {
    changeColour(new ZappoColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void taylorColour_actionPerformed(ActionEvent e)
  {
    changeColour(new TaylorColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void hydrophobicityColour_actionPerformed(ActionEvent e)
  {
    changeColour(new HydrophobicColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void helixColour_actionPerformed(ActionEvent e)
  {
    changeColour(new HelixColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void strandColour_actionPerformed(ActionEvent e)
  {
    changeColour(new StrandColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void turnColour_actionPerformed(ActionEvent e)
  {
    changeColour(new TurnColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void buriedColour_actionPerformed(ActionEvent e)
  {
    changeColour(new BuriedColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void nucleotideColour_actionPerformed(ActionEvent e)
  {
    changeColour(new NucleotideColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void applyToAllGroups_actionPerformed(ActionEvent e)
  {
    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
  }

  /**
   * DOCUMENT ME!
   *
   * @param cs DOCUMENT ME!
   */
  void changeColour(ColourSchemeI cs)
  {
    int threshold = 0;

    if(cs!=null)
    {
      if (viewport.getAbovePIDThreshold())
      {
        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                                                   "Background");

        cs.setThreshold(threshold,
                        viewport.getIgnoreGapsConsensus());

        viewport.setGlobalColourScheme(cs);
      }
      else
      {
        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
      }

      if (viewport.getConservationSelected())
      {

        Alignment al = (Alignment) viewport.alignment;
        Conservation c = new Conservation("All",
                                          ResidueProperties.propHash, 3,
                                          al.getSequences(), 0,
                                          al.getWidth() - 1);

        c.calculate();
        c.verdict(false, viewport.ConsPercGaps);

        cs.setConservation(c);

        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
            "Background"));
      }
      else
      {
        cs.setConservation(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;
          continue;
        }

        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()
            || cs instanceof PIDColourScheme
            || cs instanceof Blosum62ColourScheme)
        {
         sg.cs.setThreshold(threshold,
                viewport.getIgnoreGapsConsensus());

          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
              sg.getWidth()));
        }
        else
          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());


        if (viewport.getConservationSelected())
        {
          Conservation c = new Conservation("Group",
                                            ResidueProperties.propHash, 3,
                                            sg.sequences, 0,
                                            viewport.alignment.getWidth() - 1);
          c.calculate();
          c.verdict(false, viewport.ConsPercGaps);
          sg.cs.setConservation(c);
        }
        else
          sg.cs.setConservation(null);
      }
    }

    if (alignPanel.getOverviewPanel() != null)
    {
      alignPanel.getOverviewPanel().updateOverviewImage();
    }

    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void modifyPID_actionPerformed(ActionEvent e)
  {
    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
    {
      SliderPanel.setPIDSliderSource(alignPanel,
                                     viewport.getGlobalColourScheme(),
                                     "Background");
      SliderPanel.showPIDSlider();
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void modifyConservation_actionPerformed(ActionEvent e)
  {
    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
    {
      SliderPanel.setConservationSlider(alignPanel,
                                        viewport.globalColourScheme,
                                        "Background");
      SliderPanel.showConservationSlider();
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void conservationMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setConservationSelected(conservationMenuItem.isSelected());

    viewport.setAbovePIDThreshold(false);
    abovePIDThreshold.setSelected(false);

    changeColour(viewport.getGlobalColourScheme());

    modifyConservation_actionPerformed(null);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void abovePIDThreshold_actionPerformed(ActionEvent e)
  {
    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());

    conservationMenuItem.setSelected(false);
    viewport.setConservationSelected(false);

    changeColour(viewport.getGlobalColourScheme());

    modifyPID_actionPerformed(null);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void userDefinedColour_actionPerformed(ActionEvent e)
  {
    if (e.getActionCommand().equals("User Defined..."))
    {
      new UserDefinedColours(alignPanel, null);
    }
    else
    {
      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
          getUserColourSchemes().get(e.getActionCommand());

      changeColour(udc);
    }
  }

  public void updateUserColourMenu()
  {

    Component[] menuItems = colourMenu.getMenuComponents();
    int i, iSize = menuItems.length;
    for (i = 0; i < iSize; i++)
    {
      if (menuItems[i].getName() != null &&
          menuItems[i].getName().equals("USER_DEFINED"))
      {
        colourMenu.remove(menuItems[i]);
        iSize--;
      }
    }
    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
    {
      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
          getUserColourSchemes().keys();

      while (userColours.hasMoreElements())
      {
        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
            nextElement().toString());
        radioItem.setName("USER_DEFINED");
        radioItem.addMouseListener(new MouseAdapter()
            {
              public void mousePressed(MouseEvent evt)
              {
                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
                {
                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);

                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
                      "Remove from default list?",
                      "Remove user defined colour",
                      JOptionPane.YES_NO_OPTION);
                  if(option == JOptionPane.YES_OPTION)
                  {
                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
                    colourMenu.remove(radioItem);
                  }
                  else
                    radioItem.addActionListener(new ActionListener()
                    {
                      public void actionPerformed(ActionEvent evt)
                      {
                        userDefinedColour_actionPerformed(evt);
                      }
                    });
                }
              }
            });
        radioItem.addActionListener(new ActionListener()
        {
          public void actionPerformed(ActionEvent evt)
          {
            userDefinedColour_actionPerformed(evt);
          }
        });

        colourMenu.insert(radioItem, 15);
        colours.add(radioItem);
      }
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void PIDColour_actionPerformed(ActionEvent e)
  {
    changeColour(new PIDColourScheme());
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
  {
    changeColour(new Blosum62ColourScheme());
  }

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

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void sortIDMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
                                   HistoryItem.SORT));
    AlignmentSorter.sortByID(viewport.getAlignment());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
                                   HistoryItem.SORT));

    AlignmentSorter.sortByGroup(viewport.getAlignment());
    alignPanel.repaint();
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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);
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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;
    }

     new PCAPanel(viewport);
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("AV", "PID", "Average distance tree using PID");
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
  }

  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
  }

  /**
   * DOCUMENT ME!
   *
   * @param type DOCUMENT ME!
   * @param pwType DOCUMENT ME!
   * @param title DOCUMENT ME!
   */
  void NewTreePanel(String type, String pwType, String title)
  {
    final TreePanel tp;

    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);
  }

  /**
   * DOCUMENT ME!
   *
   * @param title DOCUMENT ME!
   * @param order DOCUMENT ME!
   */
  public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
  {
    final JMenuItem item = new JMenuItem("by " + title);
    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();
      }
    });
  }

  /**
   * Maintain the Order by->Displayed Tree menu.
   * Creates a new menu item for a TreePanel with an appropriate
   * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
   * to remove the menu item when the treePanel is closed, and adjust
   * the tree leaf to sequence mapping when the alignment is modified.
   * @param treePanel Displayed tree window.
   * @param title SortBy menu item title.
   */
  void addTreeMenuItem(final TreePanel treePanel, String title)
  {
    final JMenuItem item = new JMenuItem(title);

    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);
        }
      }
      ;
    });
  }

  /**
   * Work out whether the whole set of sequences
   * or just the selected set will be submitted for multiple alignment.
   *
   */
  private SequenceI[] gatherSequencesForAlignment()
  {
    // 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);
        }
      }
    }
    return msa;
  }

  /**
   * Decides what is submitted to a secondary structure prediction service,
   * the currently selected sequence, or the currently selected alignment
   * (where the first sequence in the set is the one that the prediction
   * will be for).
   */
  SequenceI[] gatherSeqOrMsaForSecStrPrediction()
  {
    SequenceI seq = null;
    SequenceI[] msa = null;
/*
         if (predictindex==-1) {

          JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                                "The alignment contains no columns or residues usable for prediction!",
                                                "Invalid Alignment Selection", JOptionPane.WARNING_MESSAGE);
          this.
          return;
        }
*/
    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)
    {
      return msa;
    }
    else
    {
      if (seq != null)
      {
        return new SequenceI[]
            {
            seq};
      }
    }
    return null;
  }
  /**
   * DOCUMENT ME!
   *
   * @param e DOCUMENT ME!
   */
  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");
        viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
      }
      catch (Exception ex)
      {
        JOptionPane.showMessageDialog(Desktop.desktop,
                                      "Problem reading tree file",
                                      ex.getMessage(),
                                      JOptionPane.WARNING_MESSAGE);
        ex.printStackTrace();
      }
    }
  }


  public TreePanel ShowNewickTree(NewickFile nf, String title)
  {
    return ShowNewickTree(nf,title,600,500,4,5);
  }
  /**
   * DOCUMENT ME!
   *
   * @param nf DOCUMENT ME!
   * @param title DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
  {
    TreePanel tp = null;

    try
    {
      nf.parse();

      if (nf.getTree() != null)
      {
        tp = new TreePanel(viewport,
                           viewport.getAlignment().getSequences(), nf,
                           "FromFile",
                           title);

        tp.setSize(w,h);

        if(x>0 && y>0)
          tp.setLocation(x,y);


        Desktop.addInternalFrame(tp, title, w, h);
        addTreeMenuItem(tp, title);
      }
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }

    return tp;
  }

  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();
        }
      }
    }
  }

  /**
   * Generates menu items and listener event actions for web service clients
   *
   */
  public void BuildWebServiceMenu()
  {
    if ( (Discoverer.services != null)
        && (Discoverer.services.size() > 0))
    {
      Vector msaws = (Vector) Discoverer.services.get("MsaWS");
      Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
      Vector wsmenu = new Vector();
      if (msaws != null)
      {
        // Add any Multiple Sequence Alignment Services
        final JMenu msawsmenu = new JMenu("Alignment");
        for (int i = 0, j = msaws.size(); i < j; i++)
        {
          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
              get(i);
          final JMenuItem method = new JMenuItem(sh.getName());
          method.addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e)
            {
              SequenceI[] msa = gatherSequencesForAlignment();
              new jalview.ws.MsaWSClient(sh, title, msa,
                  false, true, viewport.getAlignment().getDataset());

            }

          });
          msawsmenu.add(method);
          // Deal with services that we know accept partial alignments.
          if (sh.getName().indexOf("lustal") > -1)
          {
            // We know that ClustalWS can accept partial alignments for refinement.
            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
            methodR.addActionListener(new ActionListener()
            {
              public void actionPerformed(ActionEvent e)
              {
                SequenceI[] msa = gatherSequencesForAlignment();
                new jalview.ws.MsaWSClient(sh, title, msa,
                    true, true, viewport.getAlignment().getDataset());

              }

            });
            msawsmenu.add(methodR);

          }
        }
        wsmenu.add(msawsmenu);
      }
      if (secstrpr != null)
      {
        // Add any secondary structure prediction services
        final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
        for (int i = 0, j = secstrpr.size(); i < j; i++)
        {
          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
              secstrpr.get(i);
          final JMenuItem method = new JMenuItem(sh.getName());
          method.addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e)
            {
              SequenceI[] msa = SeqsetUtils.getNonEmptySequenceSet(gatherSeqOrMsaForSecStrPrediction());
              if (msa==null) {
                JOptionPane.showInternalMessageDialog(Desktop.desktop,
                    "There are no columns or residues usable for prediction!\n"
                    +"There must be valid residues in at least one\n"
                    +"of the sequences in the alignment,\n"
                    +"or in the currently selected region.",
                    "Invalid Input for Secondary Structure Prediction",
                    JOptionPane.WARNING_MESSAGE);
                return;
              }

              if (msa.length == 1)
              {
                // Single Sequence prediction
                new jalview.ws.JPredClient(sh,title, msa[0]);
              }
              else
              {
                if (msa.length > 1)
                {
                  // Aligned Sequences prediction
                  jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
                      title, msa);
                }
              }
            }
          });
          secstrmenu.add(method);
        }
        wsmenu.add(secstrmenu);
      }
      this.webService.removeAll();
      for (int i = 0, j = wsmenu.size(); i < j; i++)
      {
        webService.add( (JMenu) wsmenu.get(i));
      }
    }
    else
    {
      this.webService.removeAll();
      this.webService.add(this.webServiceNoServices);
    }
    // TODO: add in rediscovery function
    // TODO: reduce code redundancy.
    // TODO: group services by location as well as function.
  }

 /* public void vamsasStore_actionPerformed(ActionEvent e)
  {
    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
        getProperty("LAST_DIRECTORY"));

    chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle("Export to Vamsas file");
    chooser.setToolTipText("Export");

    int value = chooser.showSaveDialog(this);

    if (value == JalviewFileChooser.APPROVE_OPTION)
    {
      jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
    }
  }*/

  public void featureSettings_actionPerformed(ActionEvent e)
  {
    new FeatureSettings(viewport, alignPanel);
  }



public void showTranslation_actionPerformed(ActionEvent e)
{
  int s, sSize = viewport.alignment.getHeight();
  SequenceI [] newSeq = new SequenceI[sSize];

  int res, resSize;
  StringBuffer protein;
  String seq;
  for(s=0; s<sSize; s++)
  {
    protein = new StringBuffer();
    seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
    resSize = seq.length();
    for(res = 0; res < resSize; res+=3)
    {
      String codon = seq.substring(res, res+3);
      codon = codon.replace('U', 'T');
      String aa = ResidueProperties.codonTranslate(codon);
      if(aa==null)
        protein.append(viewport.getGapCharacter());
      else if(aa.equals("STOP"))
        protein.append("X");
      else
        protein.append( aa );
    }
    newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
  }


  AlignmentI al = new Alignment(newSeq);
  al.setDataset(null);


  ////////////////////////////////
  // Copy annotations across
  jalview.datamodel.AlignmentAnnotation[] annotations
      = viewport.alignment.getAlignmentAnnotation();
  int a, aSize;
  for (int i = 0; i < annotations.length; i++)
  {

    if (annotations[i].label.equals("Quality") ||
        annotations[i].label.equals("Conservation") ||
        annotations[i].label.equals("Consensus"))
    {
      continue;
    }


    aSize = viewport.alignment.getWidth()/3;
    jalview.datamodel.Annotation [] anots =
        new jalview.datamodel.Annotation[aSize];

    for(a=0; a<viewport.alignment.getWidth(); a++)
    {
     if( annotations[i].annotations[a]==null
      || annotations[i].annotations[a]==null)
       continue;

      anots[a/3] = new Annotation(
     annotations[i].annotations[a].displayCharacter,
     annotations[i].annotations[a].description,
     annotations[i].annotations[a].secondaryStructure,
     annotations[i].annotations[a].value,
     annotations[i].annotations[a].colour);
    }

    jalview.datamodel.AlignmentAnnotation aa
          = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
       annotations[i].description, anots );
     al.addAnnotation(aa);
  }


    AlignFrame af = new AlignFrame(al);
    Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
                             NEW_WINDOW_WIDTH,
                             NEW_WINDOW_HEIGHT);


   // AlignViewport newViewport = new AlignViewport(al);
   // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
   // tabbedPane.add("Protein", ap);
   // viewports.add(newViewport);
  //  alignPanels.add(ap);

    ///Dataset tab
  /////////////////////////

  //  AlignViewport ds = new AlignViewport(al.getDataset());
  //  ds.setDataset(true);
  //  AlignmentPanel dap = new AlignmentPanel(this, ds);
  //  tabbedPane.add("Dataset", dap);
  //  viewports.add(ds);
  //  alignPanels.add(dap);
  /////////////////////////


}

/*public void tabSelected()
 {
  int index = tabbedPane.getSelectedIndex();
  viewport = (AlignViewport)viewports.elementAt(index);
  alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
 }*/
}