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

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

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

import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.ws.*;

public class AlignFrame
    extends GAlignFrame
{
  public static final int NEW_WINDOW_WIDTH = 700;
  public static final int NEW_WINDOW_HEIGHT = 500;
  final AlignmentPanel alignPanel;
  final AlignViewport viewport;
  public String currentFileFormat = "Jalview";
  Stack historyList = new Stack();
  Stack redoList = new Stack();
  private int treeCount = 0;

  public AlignFrame(AlignmentI al)
  {
    viewport = new AlignViewport(al);

    alignPanel = new AlignmentPanel(this, viewport);
    alignPanel.annotationPanel.adjustPanelHeight();
    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
        annotationPanel.getPreferredSize());
    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
        getPreferredSize());
    alignPanel.setAnnotationVisible(viewport.getShowAnnotation());

    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);

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

  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
  {
    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
        getProperty(
            "LAST_DIRECTORY"),
        new String[]
        {
        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
        "jar"
    },
        new String[]
        {
        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
    }, currentFileFormat);

    chooser.setAcceptAllFileFilterUsed(false);
    chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle("Save Alignment to file");
    chooser.setToolTipText("Save");

    int value = chooser.showSaveDialog(this);

    if (value == JalviewFileChooser.APPROVE_OPTION)
    {
      currentFileFormat = chooser.getSelectedFormat();
      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                    currentFileFormat);

      if (currentFileFormat.equals("Jalview"))
      {
        String shortName = title;

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

        String choice = chooser.getSelectedFile().getPath();
        Jalview2XML.SaveState(this, choice, shortName);

        // USE Jalview2XML to save this file
        return;
      }

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

      String output = FormatAdapter.formatSequences(currentFileFormat,
          viewport.getAlignment().getSequences());

      try
      {
        java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
            FileWriter(
                choice));
        out.println(output);
        out.close();
      }
      catch (Exception ex)
      {
      }
    }
  }

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

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

  protected void createPNG_actionPerformed(ActionEvent e)
  {
    alignPanel.makePNG();
  }

  protected void epsFile_actionPerformed(ActionEvent e)
  {
    alignPanel.makeEPS();
  }

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

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

  void updateEditMenuBar()
  {
    if (historyList.size() > 0)
    {
      undoMenuItem.setEnabled(true);

      HistoryItem hi = (HistoryItem) historyList.peek();
      undoMenuItem.setText("Undo " + hi.getDescription());
    }
    else
    {
      undoMenuItem.setEnabled(false);
      undoMenuItem.setText("Undo");
    }

    if (redoList.size() > 0)
    {
      redoMenuItem.setEnabled(true);

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

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

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

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

  // used by undo and redo
  void restoreHistoryItem(HistoryItem hi)
  {
    if (hi.getType() == HistoryItem.SORT)
    {
      for (int i = 0; i < hi.getSequences().size(); i++)
      {
        viewport.alignment.getSequences().setElementAt(hi.getSequences()
            .elementAt(i),
            i);
      }
    }
    else
    {
      for (int i = 0; i < hi.getSequences().size(); i++)
      {
        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);

        if (restore.getLength() == 0)
        {
          restore.setSequence(hi.getHidden().elementAt(i).toString());
          viewport.alignment.getSequences().insertElementAt(restore,
              hi.getAlignIndex(i));
        }
        else
        {
          restore.setSequence(hi.getHidden().elementAt(i).toString());
        }
      }

      if (hi.getType() == HistoryItem.PASTE)
      {
        for (int i = viewport.alignment.getHeight() - 1;
             i > (hi.getSequences().size() - 1); i--)
        {
          viewport.alignment.deleteSequence(i);
        }
      }
    }

    updateEditMenuBar();

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

  public void moveSelectedSequences(boolean up)
  {
    SequenceGroup sg = viewport.getSelectionGroup();

    if (sg == null)
    {
      return;
    }

    if (up)
    {
      for (int i = 1; i < viewport.alignment.getHeight(); i++)
      {
        SequenceI seq = viewport.alignment.getSequenceAt(i);

        if (!sg.sequences.contains(seq))
        {
          continue;
        }

        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);

        if (sg.sequences.contains(temp))
        {
          continue;
        }

        viewport.alignment.getSequences().setElementAt(temp, i);
        viewport.alignment.getSequences().setElementAt(seq, i - 1);
      }
    }
    else
    {
      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
      {
        SequenceI seq = viewport.alignment.getSequenceAt(i);

        if (!sg.sequences.contains(seq))
        {
          continue;
        }

        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);

        if (sg.sequences.contains(temp))
        {
          continue;
        }

        viewport.alignment.getSequences().setElementAt(temp, i);
        viewport.alignment.getSequences().setElementAt(seq, i + 1);
      }
    }

    alignPanel.repaint();
  }

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

    SequenceGroup sg = viewport.getSelectionGroup();

    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
    StringBuffer buffer = new StringBuffer();

    Hashtable orderedSeqs = new Hashtable();

    for (int i = 0; i < sg.getSize(); i++)
    {
      SequenceI seq = sg.getSequenceAt(i);
      int index = viewport.alignment.findIndex(seq);
      orderedSeqs.put(index + "", seq);
    }

    int index = 0;

    for (int i = 0; i < sg.getSize(); i++)
    {
      SequenceI seq = null;

      while (seq == null)
      {
        if (orderedSeqs.containsKey(index + ""))
        {
          seq = (SequenceI) orderedSeqs.get(index + "");
          index++;

          break;
        }
        else
        {
          index++;
        }
      }

      buffer.append(seq.getName() + "\t" +
                    seq.findPosition(sg.getStartRes()) + "\t" +
                    seq.findPosition(sg.getEndRes()) + "\t" +
                    sg.getSequenceAt(i).getSequence(sg.getStartRes(),
          sg.getEndRes() + 1) + "\n");
    }

    c.setContents(new StringSelection(buffer.toString()), null);
  }

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

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

  void paste(boolean newAlignment)
  {
    try
    {
      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
      Transferable contents = c.getContents(this);

      if (contents == null)
      {
        return;
      }

      String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
      StringTokenizer st = new StringTokenizer(str);
      ArrayList seqs = new ArrayList();

      while (st.hasMoreElements())
      {
        String name = st.nextToken();
        int start = Integer.parseInt(st.nextToken());
        int end = Integer.parseInt(st.nextToken());
        Sequence sequence = new Sequence(name, st.nextToken(), start,
                                         end);

        if (!newAlignment)
        {
          viewport.alignment.addSequence(sequence);
        }
        else
        {
          seqs.add(sequence);
        }
      }

      if (newAlignment)
      {
        SequenceI[] newSeqs = new SequenceI[seqs.size()];
        seqs.toArray(newSeqs);

        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
        String newtitle = new String("Copied sequences");

        if (title.startsWith("Copied sequences"))
        {
          newtitle = title;
        }
        else
        {
          newtitle = newtitle.concat("- from " + title);
        }

        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
                                 NEW_WINDOW_HEIGHT);
      }
      else
      {
        viewport.firePropertyChange("alignment", null,
                                    viewport.getAlignment().getSequences());
        viewport.setEndSeq(viewport.alignment.getHeight());
        viewport.alignment.getWidth();
        viewport.updateConservation();
        viewport.updateConsensus();
        alignPanel.repaint();
      }
    }
    catch (Exception ex)
    {
    }

    // could be anything being pasted in here
  }

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

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

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

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

    SequenceGroup sg = viewport.getSelectionGroup();

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

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

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

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

    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());

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

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

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

  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = new SequenceGroup();

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

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

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

  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = viewport.getSelectionGroup();

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

    PaintRefresher.Refresh(null);
  }

  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
  {
    ColumnSelection colSel = viewport.getColumnSelection();

    if (colSel.size() > 0)
    {
      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
                                     HistoryItem.HIDE));

      int min = colSel.getMin();
      viewport.getAlignment().trimLeft(min);
      colSel.compensateForEdit(0, min);

      if (viewport.getSelectionGroup() != null)
      {
        viewport.getSelectionGroup().adjustForRemoveLeft(min);
      }

      Vector groups = viewport.alignment.getGroups();

      for (int i = 0; i < groups.size(); i++)
      {
        SequenceGroup sg = (SequenceGroup) groups.get(i);

        if (!sg.adjustForRemoveLeft(min))
        {
          viewport.alignment.deleteGroup(sg);
        }
      }

      alignPanel.repaint();
    }
  }

  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
  {
    ColumnSelection colSel = viewport.getColumnSelection();

    if (colSel.size() > 0)
    {
      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
                                     HistoryItem.HIDE));

      int max = colSel.getMax();
      viewport.getAlignment().trimRight(max);

      if (viewport.getSelectionGroup() != null)
      {
        viewport.getSelectionGroup().adjustForRemoveRight(max);
      }

      Vector groups = viewport.alignment.getGroups();

      for (int i = 0; i < groups.size(); i++)
      {
        SequenceGroup sg = (SequenceGroup) groups.get(i);

        if (!sg.adjustForRemoveRight(max))
        {
          viewport.alignment.deleteGroup(sg);
        }
      }

      alignPanel.repaint();
    }
  }

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

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

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

    SequenceI current;
    int jSize;

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

      for (int j = 0; j < jSize; j++)
      {
        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
        {
          current.deleteCharAt(j);
          j--;
          jSize--;
        }
      }
    }

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

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

    SequenceI current;
    int Width = viewport.getAlignment().getWidth() - 1;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  public void sequenceFeatures_actionPerformed(ActionEvent evt)
  {
    viewport.showSequenceFeatures(sequenceFeatures.isSelected());

    if (viewport.showSequenceFeatures &&
        ! ( (Alignment) viewport.alignment).featuresAdded)
    {
      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
          alignment,
          alignPanel);
      ( (Alignment) viewport.alignment).featuresAdded = true;
    }

    alignPanel.repaint();
  }

  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
  {
    if (annotationPanelMenuItem.isSelected() &&
        viewport.getWrapAlignment())
    {
      annotationPanelMenuItem.setSelected(false);

      return;
    }

    viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
    alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
  }

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

    JInternalFrame frame = new JInternalFrame();
    OverviewPanel overview = new OverviewPanel(alignPanel);
    frame.setContentPane(overview);
    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
                             frame.getWidth(), frame.getHeight());
    frame.pack();
    frame.setLayer(JLayeredPane.PALETTE_LAYER);
    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
    {
      public void internalFrameClosed(
          javax.swing.event.InternalFrameEvent evt)
      {
        alignPanel.setOverviewPanel(null);
      }
      ;
    });

    alignPanel.setOverviewPanel(overview);
  }

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

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

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

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

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

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

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

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

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

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

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

  void changeColour(ColourSchemeI cs)
  {
    int threshold = 0;

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

      if (cs instanceof ResidueColourScheme)
      {
        ( (ResidueColourScheme) cs).setThreshold(threshold);
      }
      else if (cs instanceof ScoreColourScheme)
      {
        ( (ScoreColourScheme) cs).setThreshold(threshold);
      }

      viewport.setGlobalColourScheme(cs);
    }
    else if (cs instanceof ResidueColourScheme)
    {
      ( (ResidueColourScheme) cs).setThreshold(0);
    }
    else if (cs instanceof ScoreColourScheme)
    {
      ( (ScoreColourScheme) cs).setThreshold(0);
    }

    if (viewport.getConservationSelected())
    {
      ConservationColourScheme ccs = null;

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

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

      ccs = new ConservationColourScheme(c, cs);

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

      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
                                                  "Background");
    }
    else
    {
      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
      if (cs != null)
      {
        cs.setConsensus(viewport.vconsensus);
      }

      viewport.setGlobalColourScheme(cs);
    }

    if (viewport.getColourAppliesToAllGroups())
    {
      Vector groups = viewport.alignment.getGroups();

      for (int i = 0; i < groups.size(); i++)
      {
        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);

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

        if (viewport.getAbovePIDThreshold())
        {
          if (sg.cs instanceof ResidueColourScheme)
          {
            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
          }
          else if (sg.cs instanceof ScoreColourScheme)
          {
            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
          }

          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
              sg.getWidth()));
        }

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

          ConservationColourScheme ccs = new ConservationColourScheme(c,
              sg.cs);

          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                                 sg.getWidth()));
          sg.cs = ccs;
        }
        else if (cs != null)
        {
          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
              sg.getWidth()));
        }
      }
    }

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

    alignPanel.repaint();
  }

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

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

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

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

    ColourSchemeI cs = viewport.getGlobalColourScheme();

    if (cs instanceof ConservationColourScheme)
    {
      changeColour( ( (ConservationColourScheme) cs).cs);
    }
    else
    {
      changeColour(cs);
    }

    modifyConservation_actionPerformed(null);
  }

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

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

    ColourSchemeI cs = viewport.getGlobalColourScheme();

    if (cs instanceof ConservationColourScheme)
    {
      changeColour( ( (ConservationColourScheme) cs).cs);
    }
    else
    {
      changeColour(cs);
    }

    modifyPID_actionPerformed(null);
  }

  public void userDefinedColour_actionPerformed(ActionEvent e)
  {
    new UserDefinedColours(alignPanel, null);
  }

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

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

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

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

  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
  {
    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
                                   HistoryItem.SORT));

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

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

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

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

      return;
    }

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

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

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

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

  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
  }

  void NewTreePanel(String type, String pwType, String title)
  {
    String ltitle;
    final TreePanel tp;

    if ( (viewport.getSelectionGroup() != null) &&
        (viewport.getSelectionGroup().getSize() > 3))
    {
      int s = 0;
      SequenceGroup sg = viewport.getSelectionGroup();

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

          return;
        }
      }

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

        return;
      }

      tp = new TreePanel(viewport,
                         viewport.getAlignment().getSequences(), type, pwType,
                         0,
                         viewport.alignment.getWidth());
    }

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

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

  public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
  {
    final JMenuItem item = new JMenuItem("by " + title);
    sort.add(item);
    item.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
                                       HistoryItem.SORT));

        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
        AlignmentSorter.sortBy(viewport.getAlignment(), order);
        alignPanel.repaint();
      }
    });
  }

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

    treeCount++;

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

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

    treePanel.addInternalFrameListener(new javax.swing.event.
                                       InternalFrameAdapter()
    {
      public void internalFrameClosed(
          javax.swing.event.InternalFrameEvent evt)
      {
        treeCount--;
        sortByTreeMenu.remove(item);

        if (treeCount == 0)
        {
          sort.remove(sortByTreeMenu);
        }
      }
      ;
    });
    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
    {
      public void propertyChange(PropertyChangeEvent evt)
      {
        if (evt.getPropertyName().equals("alignment"))
        {
          treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
          treePanel.repaint();
        }
      }
    });
  }

  public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
  {
    // TODO:resolve which menu item was actually selected
    // Now, check we have enough sequences
    SequenceI[] msa = null;

    if ( (viewport.getSelectionGroup() != null) &&
        (viewport.getSelectionGroup().getSize() > 1))
    {
      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
      SequenceGroup seqs = viewport.getSelectionGroup();
      int sz;
      msa = new SequenceI[sz = seqs.getSize()];

      for (int i = 0; i < sz; i++)
      {
        msa[i] = (SequenceI) seqs.getSequenceAt(i);
      }
    }
    else
    {
      Vector seqs = viewport.getAlignment().getSequences();

      if (seqs.size() > 1)
      {
        msa = new SequenceI[seqs.size()];

        for (int i = 0; i < seqs.size(); i++)
        {
          msa[i] = (SequenceI) seqs.elementAt(i);
        }
      }
    }

    if (msa != null)
    {
      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
          title, msa, false, true);
    }
  }

  public void ClustalRealign_actionPerformed(ActionEvent e)
  {
    // TODO:resolve which menu item was actually selected
    // Now, check we have enough sequences
    SequenceI[] msa = null;

    if ( (viewport.getSelectionGroup() != null) &&
        (viewport.getSelectionGroup().getSize() > 1))
    {
      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
      SequenceGroup seqs = viewport.getSelectionGroup();
      int sz;
      msa = new SequenceI[sz = seqs.getSize()];

      for (int i = 0; i < sz; i++)
      {
        msa[i] = (SequenceI) seqs.getSequenceAt(i);
      }
    }
    else
    {
      Vector seqs = viewport.getAlignment().getSequences();

      if (seqs.size() > 1)
      {
        msa = new SequenceI[seqs.size()];

        for (int i = 0; i < seqs.size(); i++)
        {
          msa[i] = (SequenceI) seqs.elementAt(i);
        }
      }
    }

    if (msa != null)
    {
      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
          title, msa, true, true);
    }
  }

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

    if ( (viewport.getSelectionGroup() != null) &&
        (viewport.getSelectionGroup().getSize() > 0))
    {
      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
      SequenceGroup seqs = viewport.getSelectionGroup();

      if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
      {
        seq = (SequenceI) seqs.getSequenceAt(0);
      }
      else
      {
        int sz;
        msa = new SequenceI[sz = seqs.getSize()];

        for (int i = 0; i < sz; i++)
        {
          msa[i] = (SequenceI) seqs.getSequenceAt(i);
        }
      }
    }
    else
    {
      Vector seqs = viewport.getAlignment().getSequences();

      if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
      {
        seq = (SequenceI) seqs.elementAt(0);
      }
      else
      {
        msa = new SequenceI[seqs.size()];

        for (int i = 0; i < seqs.size(); i++)
        {
          msa[i] = (SequenceI) seqs.elementAt(i);
        }
      }
    }

    if (msa != null)
    {
      JPredClient ct = new JPredClient(title, msa);
    }
    else if (seq != null)
    {
      JPredClient ct = new JPredClient(title, seq);
    }
    else
    {
      System.err.print(
          "JALVIEW ERROR! - Unexpected JPred selection state!\n");
    }
  }

  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
  {
    // TODO:resolve which menu item was actually selected
    // Now, check we have enough sequences
    SequenceI[] msa = null;

    if ( (viewport.getSelectionGroup() != null) &&
        (viewport.getSelectionGroup().getSize() > 1))
    {
      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
      SequenceGroup seqs = viewport.getSelectionGroup();
      int sz;
      msa = new SequenceI[sz = seqs.getSize()];

      for (int i = 0; i < sz; i++)
      {
        msa[i] = (SequenceI) seqs.getSequenceAt(i);
      }
    }
    else
    {
      Vector seqs = viewport.getAlignment().getSequences();

      if (seqs.size() > 1)
      {
        msa = new SequenceI[seqs.size()];

        for (int i = 0; i < seqs.size(); i++)
        {
          msa[i] = (SequenceI) seqs.elementAt(i);
        }
      }
    }

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

  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
  {
    // Pick the tree file
    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
        getProperty(
            "LAST_DIRECTORY"));
    chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle("Select a newick-like tree file");
    chooser.setToolTipText("Load a tree file");

    int value = chooser.showOpenDialog(null);

    if (value == JalviewFileChooser.APPROVE_OPTION)
    {
      String choice = chooser.getSelectedFile().getPath();
      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);

      try
      {
        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
            "File");
        ShowNewickTree(fin, choice);
      }
      catch (Exception ex)
      {
        JOptionPane.showMessageDialog(Desktop.desktop,
                                      "Problem reading tree file",
                                      ex.getMessage(),
                                      JOptionPane.WARNING_MESSAGE);
        ex.printStackTrace();
      }
    }
  }

  public void ShowNewickTree(NewickFile nf, String title)
  {
    try
    {
      nf.parse();

      if (nf.getTree() != null)
      {
        TreePanel tp = new TreePanel(viewport,
                                     viewport.getAlignment().getSequences(), nf,
                                     "FromFile",
                                     title);
        Desktop.addInternalFrame(tp, title, 600, 500);
        addTreeMenuItem(tp, title);
        viewport.setCurrentTree(tp.getTree());
      }
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  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();
        }
      }
    }
  }
}