/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 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 jalview.analysis.*;

import jalview.datamodel.*;

import jalview.io.*;

import jalview.jbgui.*;

import org.jibble.epsgraphics.*;

import java.awt.*;
import java.awt.event.*;
import java.awt.image.*;

import java.io.*;

import java.util.*;

import javax.swing.*;
import javax.imageio.*;

import java.beans.PropertyChangeEvent;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class TreePanel extends GTreePanel
{
    String type;
    String pwtype;
    TreeCanvas treeCanvas;
    NJTree tree;
    AlignViewport av;

    /**
     * Creates a new TreePanel object.
     *
     * @param av DOCUMENT ME!
     * @param seqVector DOCUMENT ME!
     * @param type DOCUMENT ME!
     * @param pwtype DOCUMENT ME!
     * @param s DOCUMENT ME!
     * @param e DOCUMENT ME!
     */
    public TreePanel(AlignmentPanel ap, String type, String pwtype)
    {
      super();
      initTreePanel(ap, type, pwtype, null, null);

      // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
      // showDistances(true);
    }

    /**
     * Creates a new TreePanel object.
     *
     * @param av DOCUMENT ME!
     * @param seqVector DOCUMENT ME!
     * @param newtree DOCUMENT ME!
     * @param type DOCUMENT ME!
     * @param pwtype DOCUMENT ME!
     */
    public TreePanel(AlignmentPanel ap,
                     String type,
                     String pwtype,
                     NewickFile newtree)
    {
      super();
      initTreePanel(ap, type, pwtype, newtree, null);
    }

    public TreePanel(AlignmentPanel av,
        String type,
        String pwtype,
        NewickFile newtree, AlignmentView inputData) {
     super();
     initTreePanel(av,type,pwtype,newtree,inputData);
    }

    public AlignmentI getAlignment()
    {
      return treeCanvas.av.getAlignment();
    }
    public AlignViewport getViewPort() {
      return treeCanvas.av;
    }

    void initTreePanel(AlignmentPanel ap, String type,  String pwtype,
                       NewickFile newTree, AlignmentView inputData)
    {

      av = ap.av;
      this.type = type;
      this.pwtype = pwtype;

      treeCanvas = new TreeCanvas(this, ap, scrollPane);
      scrollPane.setViewportView(treeCanvas);

      PaintRefresher.Register(this, ap.av.getSequenceSetId());

      buildAssociatedViewMenu();

      av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
      {
        public void propertyChange(PropertyChangeEvent evt)
        {
          if (evt.getPropertyName().equals("alignment"))
          {
            if(tree==null)
              System.out.println("tree is null");
            if(evt.getNewValue()==null)
              System.out.println("new alignment sequences vector value is null");

            tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
            treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
            repaint();
          }
        }
      });

      TreeLoader tl = new TreeLoader(newTree);
      if (inputData!=null) {
        tl.odata=inputData;
      }
      tl.start();

    }

    public void viewMenu_menuSelected()
    {
      buildAssociatedViewMenu();
    }


    void buildAssociatedViewMenu()
    {
      AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
      if(aps.length==1 && treeCanvas.ap==aps[0])
      {
        associateLeavesMenu.setVisible(false);
        return;
      }

      associateLeavesMenu.setVisible(true);

      if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
      {
        viewMenu.insertSeparator(viewMenu.getItemCount()-1);
      }

      associateLeavesMenu.removeAll();


      JRadioButtonMenuItem item;
      ButtonGroup buttonGroup = new ButtonGroup();
      int i, iSize = aps.length;
      final TreePanel thisTreePanel = this;
      for(i=0; i<iSize; i++)
      {
          final AlignmentPanel ap = aps[i];
          item = new JRadioButtonMenuItem(ap.av.viewName, ap==treeCanvas.ap );
          buttonGroup.add(item);
          item.addActionListener(new ActionListener()
              {
                public void actionPerformed(ActionEvent evt)
                {
                  treeCanvas.applyToAllViews = false;
                  treeCanvas.ap = ap;
                  treeCanvas.av = ap.av;
                  PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
                }
              });

          associateLeavesMenu.add(item);
      }

      final JRadioButtonMenuItem itemf =
          new JRadioButtonMenuItem("All Views", treeCanvas.applyToAllViews);
      buttonGroup.add(itemf);
      itemf.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent evt)
        {
          treeCanvas.applyToAllViews = itemf.isSelected();
        }
      });
      associateLeavesMenu.add(itemf);

    }

    class TreeLoader extends Thread
    {
      NewickFile newtree;
      jalview.datamodel.AlignmentView odata=null;
      public TreeLoader(NewickFile newtree)
      {
        this.newtree = newtree;
        if (newtree != null)
        {
          // Must be outside run(), as Jalview2XML tries to
          // update distance/bootstrap visibility at the same time
          showBootstrap(newtree.HasBootstrap());
          showDistances(newtree.HasDistances());
        }
      }

      public void run()
      {

        if(newtree!=null)
        {
          if (odata==null) {
            tree = new NJTree(av.alignment.getSequencesArray(),
                              newtree);
          } else {
            tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
          }
          if (!tree.hasOriginalSequenceData())
            allowOriginalSeqData(false);
        }
        else
        {
          int start, end;
          SequenceI [] seqs;
          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
          if(av.getSelectionGroup()==null)
          {
            start = 0;
            end = av.alignment.getWidth();
            seqs = av.alignment.getSequencesArray();
          }
          else
          {
            start = av.getSelectionGroup().getStartRes();
            end = av.getSelectionGroup().getEndRes()+1;
            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
          }

          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
          showDistances(true);
        }


        tree.reCount(tree.getTopNode());
        tree.findHeight(tree.getTopNode());
        treeCanvas.setTree(tree);
        treeCanvas.repaint();
        av.setCurrentTree(tree);

      }
    }

    public void showDistances(boolean b)
    {
      treeCanvas.setShowDistances(b);
      distanceMenu.setSelected(b);
    }

    public void showBootstrap(boolean b)
    {
      treeCanvas.setShowBootstrap(b);
      bootstrapMenu.setSelected(b);
    }

    public void showPlaceholders(boolean b)
    {
      placeholdersMenu.setState(b);
      treeCanvas.setMarkPlaceholders(b);
    }

    private void allowOriginalSeqData(boolean b) {
      originalSeqData.setVisible(b);
    }



    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public NJTree getTree()
    {
        return tree;
    }


    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void textbox_actionPerformed(ActionEvent e)
    {
        CutAndPasteTransfer cap = new CutAndPasteTransfer();

        StringBuffer buffer = new StringBuffer();

        if (type.equals("AV"))
        {
            buffer.append("Average distance tree using ");
        }
        else
        {
            buffer.append("Neighbour joining tree using ");
        }

        if (pwtype.equals("BL"))
        {
            buffer.append("BLOSUM62");
        }
        else
        {
            buffer.append("PID");
        }

        Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);

        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void saveAsNewick_actionPerformed(ActionEvent e)
    {
        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
                    "LAST_DIRECTORY"));
        chooser.setFileView(new JalviewFileView());
        chooser.setDialogTitle("Save tree as newick file");
        chooser.setToolTipText("Save");

        int value = chooser.showSaveDialog(null);

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

            try
            {
                jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
                String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
                java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
                            choice));
                out.println(output);
                out.close();
            }
            catch (Exception ex)
            {
                ex.printStackTrace();
            }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void printMenu_actionPerformed(ActionEvent e)
    {
        //Putting in a thread avoids Swing painting problems
        treeCanvas.startPrinting();
    }


    public void originalSeqData_actionPerformed(ActionEvent e)
    {
      if (!tree.hasOriginalSequenceData())
      {
        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
        return;
      }
      // decide if av alignment is sufficiently different to original data to warrant a new window to be created
      // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
      // or create a selection box around columns in alignment view
      // test Alignment(SeqCigar[])
      Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
          getGapCharacter());


      if (alAndColsel != null && alAndColsel[0]!=null)
       {
         // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);

         Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
         Alignment dataset = av.getAlignment().getDataset();
         if (dataset != null)
         {
           al.setDataset(dataset);
         }

         if (true)
         {
           // make a new frame!
           AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
                                           AlignFrame.DEFAULT_WIDTH,
                                           AlignFrame.DEFAULT_HEIGHT
);

           //>>>This is a fix for the moment, until a better solution is found!!<<<
           // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());

       //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
       //                                     msaorder);

           Desktop.addInternalFrame(af, "Original Data for " + this.title,
                                    AlignFrame.DEFAULT_WIDTH,
                                    AlignFrame.DEFAULT_HEIGHT);
         }
       }
    }


    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void fitToWindow_actionPerformed(ActionEvent e)
    {
        treeCanvas.fitToWindow = fitToWindow.isSelected();
        repaint();
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void font_actionPerformed(ActionEvent e)
    {
        if (treeCanvas == null)
        {
            return;
        }

        new FontChooser(this);
    }

    public Font getTreeFont()
    {
        return treeCanvas.font;
    }

    public void setTreeFont(Font font)
    {
      if(treeCanvas!=null)
      treeCanvas.setFont(font);
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void distanceMenu_actionPerformed(ActionEvent e)
    {
        treeCanvas.setShowDistances(distanceMenu.isSelected());
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void bootstrapMenu_actionPerformed(ActionEvent e)
    {
        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void placeholdersMenu_actionPerformed(ActionEvent e)
    {
        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void epsTree_actionPerformed(ActionEvent e)
    {
      boolean accurateText = true;

      String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
          "Prompt each time");

    // If we need to prompt, and if the GUI is visible then
    // Prompt for EPS rendering style
      if (renderStyle.equalsIgnoreCase("Prompt each time")
          && !
          (System.getProperty("java.awt.headless") != null
           && System.getProperty("java.awt.headless").equals("true")))
      {
        EPSOptions eps = new EPSOptions();
        renderStyle = eps.getValue();

        if (renderStyle==null || eps.cancelled)
          return;


      }

      if (renderStyle.equalsIgnoreCase("text"))
      {
        accurateText = false;
      }

        int width = treeCanvas.getWidth();
        int height = treeCanvas.getHeight();

        try
        {
            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
                        "LAST_DIRECTORY"), new String[] { "eps" },
                    new String[] { "Encapsulated Postscript" },
                    "Encapsulated Postscript");
            chooser.setFileView(new jalview.io.JalviewFileView());
            chooser.setDialogTitle("Create EPS file from tree");
            chooser.setToolTipText("Save");

            int value = chooser.showSaveDialog(this);

            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
            {
                return;
            }

            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
                                          chooser.getSelectedFile().getParent());

            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
            EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
                                                 height);

            pg.setAccurateTextMode(accurateText);

            treeCanvas.draw(pg, width, height);

            pg.flush();
            pg.close();
        }
        catch (Exception ex)
        {
            ex.printStackTrace();
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void pngTree_actionPerformed(ActionEvent e)
    {
        int width = treeCanvas.getWidth();
        int height = treeCanvas.getHeight();

        try
        {
            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
                        "LAST_DIRECTORY"), new String[] { "png" },
                    new String[] { "Portable network graphics" },
                    "Portable network graphics");

            chooser.setFileView(new jalview.io.JalviewFileView());
            chooser.setDialogTitle("Create PNG image from tree");
            chooser.setToolTipText("Save");

            int value = chooser.showSaveDialog(this);

            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
            {
                return;
            }

            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
                chooser.getSelectedFile().getParent());

            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());

            BufferedImage bi = new BufferedImage(width, height,
                    BufferedImage.TYPE_INT_RGB);
            Graphics png = bi.getGraphics();

            treeCanvas.draw(png, width, height);

            ImageIO.write(bi, "png", out);
            out.close();
        }
        catch (Exception ex)
        {
            ex.printStackTrace();
        }
    }
}