/*
 * 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.appletgui;

import jalview.jbappletgui.GAlignFrame;
import jalview.schemes.*;
import jalview.datamodel.*;
import jalview.analysis.*;
import jalview.io.*;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import java.io.InputStreamReader;
import java.io.BufferedReader;

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;
  jalview.bin.JalviewLite applet;

  public AlignFrame(AlignmentI al)
  {
    this.applet = null;
    viewport = new AlignViewport(al, null);
    alignPanel = new AlignmentPanel(this, viewport);
    add(alignPanel);
    alignPanel.validate();

    this.addWindowListener(new WindowAdapter()
    {
      public void windowClosing(WindowEvent e)
      {
        closeMenuItem_actionPerformed(null);
      }
    });

  }


  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
  {
    this.applet = applet;
    viewport = new AlignViewport(al, applet);
    alignPanel = new AlignmentPanel(this, viewport);
    add(alignPanel);
    alignPanel.validate();

    String treeFile = applet.getParameter("treeFile");
    if (treeFile != null)
    {
      try
      {
        treeFile = treeFile;
        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
            getCodeBase() + treeFile, "URL");
        fin.parse();

        if (fin.getTree() != null)
        {
          TreePanel tp = null;
          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
                             fin, "FromFile", applet.getCodeBase() + treeFile);
          jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
          addTreeMenuItem(tp, treeFile);
        }
      }
      catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }

    this.addWindowListener(new WindowAdapter()
    {
      public void windowClosing(WindowEvent e)
          {
            closeMenuItem_actionPerformed(null);
          }
    });



  }

  public void inputText_actionPerformed(ActionEvent e)
  {
    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
    Frame frame = new Frame();
    frame.add(cap);
    jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
  }

  protected void outputText_actionPerformed(ActionEvent e)
  {
    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
    Frame frame = new Frame();
    frame.add(cap);
    jalview.bin.JalviewLite.addFrame(frame,
                                     "Alignment output - " + e.getActionCommand(),
                                     600, 500);
    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
                                              viewport.getAlignment().
                                              getSequences()));
  }

  public void closeMenuItem_actionPerformed(ActionEvent e)
  {
    PaintRefresher.components.remove(viewport.alignment);
    dispose();
  }

  Stack historyList = new Stack();
  Stack redoList = new Stack();

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

    if (redoList.size() > 0)
    {
      redoMenuItem.setEnabled(true);
      HistoryItem hi = (HistoryItem) redoList.peek();
      redoMenuItem.setLabel("Redo " + hi.getDescription());
    }
    else
    {
      redoMenuItem.setEnabled(false);
      redoMenuItem.setLabel("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)
        {
          // log.System.out.println(hi.getHidden().elementAt(i));
          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();
  }

  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();
  }

  StringBuffer copiedSequences;
  protected void copy_actionPerformed(ActionEvent e)
  {
    if (viewport.getSelectionGroup() == null)
    {
      return;
    }

    SequenceGroup sg = viewport.getSelectionGroup();
    copiedSequences = 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, 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;
        }

        copiedSequences.append(seq.getName() + "\t" +
            startRes + "\t" +
            endRes + "\t" +
            seq.getSequence(sg.getStartRes(),
                sg.getEndRes() + 1) + "\n");
    }

  }

  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
    {
      if (copiedSequences == null)
      {
        return;
      }

      StringTokenizer st = new StringTokenizer(copiedSequences.toString());
      Vector seqs = new Vector();
      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.addElement(sequence);
        }
      }

      if (newAlignment)
      {
        SequenceI[] newSeqs = new SequenceI[seqs.size()];
        for (int i = 0; i < seqs.size(); i++)
        {
          newSeqs[i] = (SequenceI) seqs.elementAt(i);
        }

        AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
        String newtitle = new String("Copied sequences");
        if (getTitle().startsWith("Copied sequences"))
        {
          newtitle = getTitle();
        }
        else
        {
          newtitle = newtitle.concat("- from " + getTitle());
        }
        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
                                         NEW_WINDOW_HEIGHT);
      }
      else
      {
        viewport.setEndSeq(viewport.alignment.getHeight());
        viewport.alignment.getWidth();
        viewport.updateConservation();
        viewport.updateConsensus();
        alignPanel.repaint();
      }

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

  }

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

  protected void delete_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
                                   HistoryItem.HIDE));
    if (viewport.getSelectionGroup() == null)
    {
      return;
    }


    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.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
    if (viewport.getAlignment().getHeight() < 1)
    {
      try
      {
        this.setVisible(false);
      }
      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), false);
    }
    sg.setEndRes(viewport.alignment.getWidth()-1);
    viewport.setSelectionGroup(sg);
    alignPanel.repaint();
    PaintRefresher.Refresh(null, viewport.alignment);
  }

  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setSelectionGroup(null);
    viewport.getColumnSelection().clear();
    viewport.setSelectionGroup(null);
    PaintRefresher.Refresh(null, viewport.alignment);
  }

  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), false);
    }

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

  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.elementAt(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.elementAt(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();
    resetAllClustalSchemes();
    alignPanel.repaint();
  }

  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                   HistoryItem.HIDE));

    SequenceI current;
    int jSize;

    Vector seqs=null;

    int start=0, 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();
    }
    else
      seqs = viewport.alignment.getSequences();

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

      int j = start;
      do
      {
        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
        {
          current.deleteCharAt(j);
          j--;
          jSize--;
        }
        j++;
      }
      while(j < end && j < jSize) ;
    }

    resetAllClustalSchemes();
    viewport.updateConservation();
    viewport.updateConsensus();
    alignPanel.repaint();
  }

  void resetAllClustalSchemes()
  {
    if(viewport.getGlobalColourScheme()!=null
       && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
    {
      ((ClustalxColourScheme)viewport.getGlobalColourScheme()).
          resetClustalX(viewport.alignment.getSequences(),
                        viewport.alignment.getWidth());
    }

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



  public void findMenuItem_actionPerformed(ActionEvent e)
  {
    Finder finder = new Finder(alignPanel);
  }

  public void font_actionPerformed(ActionEvent e)
  {
    Frame frame = new Frame();
    FontChooser fc = new FontChooser(alignPanel, frame);
    frame.add(fc);
    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);

  }

  protected void fullSeqId_actionPerformed(ActionEvent e)
  {
    viewport.setShowFullId(fullSeqId.getState());
    alignPanel.fontChanged();
    alignPanel.repaint();
  }

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

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

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

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

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

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

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

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

  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
  {
    if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
    {
      annotationPanelMenuItem.setState(false);
      return;
    }
    viewport.setShowAnnotation(annotationPanelMenuItem.getState());
    alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
  }

  public void overviewMenuItem_actionPerformed(ActionEvent e)
  {
    if (alignPanel.overviewPanel != null)
    {
      return;
    }

    Frame frame = new Frame();
    OverviewPanel overview = new OverviewPanel(alignPanel);
    frame.add(overview);
    // +50 must allow for applet frame window
    jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
                                     overview.preferredSize().width,
                                     overview.preferredSize().height + 50);

    frame.pack();
    frame.addWindowListener(new WindowAdapter()
    {
      public void windowClosing(WindowEvent e)
      {
        alignPanel.setOverviewPanel(null);
      };
    });

    alignPanel.setOverviewPanel(overview);

  }

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

  public void clustalColour_actionPerformed(ActionEvent e)
  {
    abovePIDThreshold.setState(false);
    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.getState());
  }

  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
        {
          try
          {
            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
          }
          catch (Exception ex)
          {
            ex.printStackTrace();
            sg.cs = cs;
          }
        }

        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);
          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
        }

      }
    }


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

    alignPanel.repaint();
  }



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

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

  protected void conservationMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setConservationSelected(conservationMenuItem.getState());

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

    changeColour(viewport.getGlobalColourScheme());

    modifyConservation_actionPerformed(null);
  }

  public void abovePIDThreshold_actionPerformed(ActionEvent e)
  {
    viewport.setAbovePIDThreshold(abovePIDThreshold.getState());

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

    changeColour(viewport.getGlobalColourScheme());

    modifyPID_actionPerformed(null);
  }

  public void userDefinedColour_actionPerformed(ActionEvent e)
  {
    UserDefinedColours chooser = 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());
    alignPanel.repaint();

  }

  public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
  {
    RedundancyPanel sp = new RedundancyPanel(alignPanel);
    Frame frame = new Frame();
    frame.add(sp);
    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
                                     400, 120);

  }

  public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
  {
    if (viewport.getSelectionGroup().getSize() > 1)
    {
      Frame frame = new Frame();
      frame.add(new PairwiseAlignPanel(viewport));
      jalview.bin.JalviewLite.addFrame(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)
    {
      return;
    }

    try
    {
      PCAPanel pcaPanel = new PCAPanel(viewport, null);
      Frame frame = new Frame();
      frame.add(pcaPanel);
      jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
                                       400, 400);
    }
    catch (java.lang.OutOfMemoryError ex)
    {
    }

  }

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

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

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

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

  void NewTreePanel(String type, String pwType, String title)
  {
    //are the sequences aligned?
    if (!viewport.alignment.isAligned())
    {
      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());
        }
      }
      alignPanel.repaint();

    }

    final TreePanel tp;
    if (viewport.getSelectionGroup() != null &&
        viewport.getSelectionGroup().getSize() > 3)
    {
      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
                         pwType,
                         0, viewport.alignment.getWidth());
    }
    else
    {
      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
                         type, pwType, 0, viewport.alignment.getWidth());
    }

    addTreeMenuItem(tp, title);

    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
  }

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

    treePanel.addWindowListener(new WindowAdapter()
    {
      public void windowClosing(WindowEvent e)
      {
        sortByTreeMenu.remove(item);
      };
    });
  }

  protected void documentation_actionPerformed(ActionEvent e)
  {
    jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
  }

  protected void about_actionPerformed(ActionEvent e)
  {

    class AboutPanel extends Canvas
    {
      String version;
      public AboutPanel(String version)
      { this.version = version; }

      public void paint(Graphics g)
      {
        g.setColor(Color.white);
        g.fillRect(0, 0, getSize().width, getSize().height);
        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
        FontMetrics fm = g.getFontMetrics();
        int fh = fm.getHeight();
        int y = 5, x = 7;
        g.setColor(Color.black);
        g.setFont(new Font("Helvetica", Font.BOLD, 14));
        g.drawString("Jalview - Release "+version, 200, y += fh);
        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
        g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
                     x, y += fh * 2);
        g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
                     x, y += fh);
        g.drawString(
            "For any issues relating to Jalview, email help@jalview.org", x,
            y += fh);
        g.drawString("If  you use JalView, please cite:", x, y += fh + 8);
        g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
                     x, y += fh);
        g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);
      }
    }

    String version = "test";
    java.net.URL url = getClass().getResource("/.build_properties");
    if (url != null)
    {
      try
      {
        BufferedReader reader = new BufferedReader(new InputStreamReader(
            url.openStream()));
        String line;
        while ( (line = reader.readLine()) != null)
        {
          if (line.indexOf("VERSION") > -1)
          {
            version = line.substring(line.indexOf("=") + 1);
          }
        }
      }
      catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }


    Frame frame = new Frame();
    frame.add(new AboutPanel(version));
    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);

  }
}