/*
 * 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 java.util.*;

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

import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.io.*;

public class TreePanel extends Frame implements ActionListener, ItemListener
{
  SequenceI[] seq;
  String type;
  String pwtype;
  int start;
  int end;
  TreeCanvas treeCanvas;
  NJTree tree;
  AlignViewport av;

  public NJTree getTree()
  {
    return tree;
  }

  /**
   * 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(AlignViewport av, String type, String pwtype)
  {
    try
    {
      jbInit();
      this.setMenuBar(jMenuBar1);
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }

    initTreePanel(av, type, pwtype, null);
  }

  /**
   * 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(AlignViewport av,
                   String type,
                   String pwtype,
                   NewickFile newtree)
  {
    try
    {
      jbInit();
      this.setMenuBar(jMenuBar1);
    }
    catch (Exception e)
    {
      e.printStackTrace();
    }

    initTreePanel(av, type, pwtype, newtree);
  }


  void initTreePanel(AlignViewport av,
                     String type,
                     String pwtype,
                     NewickFile newTree)
  {

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

    treeCanvas = new TreeCanvas(av, scrollPane);
    scrollPane.add(treeCanvas);


    TreeLoader tl = new TreeLoader(newTree);
    tl.start();

  }

  class TreeLoader extends Thread
  {
    NewickFile newtree;

    public TreeLoader(NewickFile newtree)
    {
      this.newtree = newtree;
    }

    public void run()
    {
      if (newtree != null)
        tree = new NJTree(av.alignment.getSequencesArray(),
                          newtree);
      else
        {
          int start, end;
          SequenceI [] seqs;
          CigarArray seqStrings = null;
        //  if (av.hasHiddenColumns)
          {
        //    seqStrings = av.getSelectionAsString();
          }

          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);
        }

      tree.reCount(tree.getTopNode());
      tree.findHeight(tree.getTopNode());
      treeCanvas.setTree(tree);
      if(newtree!=null)
      {
        distanceMenu.setState(newtree.HasDistances());
        bootstrapMenu.setState(newtree.HasBootstrap());
        treeCanvas.setShowBootstrap(newtree.HasBootstrap());
        treeCanvas.setShowDistances(newtree.HasDistances());
      }


      treeCanvas.repaint();

      av.setCurrentTree(tree);

    }
  }

  public void actionPerformed(ActionEvent evt)
  {
    if(evt.getSource()==newickOutput)
      newickOutput_actionPerformed();
    else if(evt.getSource()==fontSize)
      fontSize_actionPerformed();
  }

  public void itemStateChanged(ItemEvent evt)
  {
    if(evt.getSource()==fitToWindow)
      treeCanvas.fitToWindow = fitToWindow.getState();

    else if(evt.getSource()==distanceMenu)
      treeCanvas.setShowDistances(distanceMenu.getState());

    else if(evt.getSource()==bootstrapMenu)
      treeCanvas.setShowBootstrap(bootstrapMenu.getState());

    else if(evt.getSource()==placeholdersMenu)
      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());

    treeCanvas.repaint();
  }


  public void newickOutput_actionPerformed()
  {
    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
    String output = fout.print(false, true);
    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
    cap.setText(output);
    java.awt.Frame frame = new java.awt.Frame();
    frame.add(cap);
    jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
  }

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

  public void setTreeFont(java.awt.Font font)
  {
    treeCanvas.font = font;
    treeCanvas.repaint();
  }

  protected void fontSize_actionPerformed()
  {
     if( treeCanvas==null )
        return;

    new FontChooser(this);
  }




  BorderLayout borderLayout1 = new BorderLayout();
  protected ScrollPane scrollPane = new ScrollPane();
  MenuBar jMenuBar1 = new MenuBar();
  Menu jMenu2 = new Menu();
  protected MenuItem fontSize = new MenuItem();
  protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
  protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
  protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
  protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
  Menu fileMenu = new Menu();
  MenuItem newickOutput = new MenuItem();

  private void jbInit() throws Exception {
      setLayout(borderLayout1);
      this.setBackground(Color.white);
      this.setFont(new java.awt.Font("Verdana", 0, 12));
      jMenu2.setLabel("View");
      fontSize.setLabel("Font...");
      fontSize.addActionListener(this);
      bootstrapMenu.setLabel("Show Bootstrap Values");
      bootstrapMenu.addItemListener(this);
      distanceMenu.setLabel("Show Distances");
      distanceMenu.addItemListener(this);
      placeholdersMenu.setLabel("Mark Unassociated Leaves");
      placeholdersMenu.addItemListener(this);
      fitToWindow.setState(true);
      fitToWindow.setLabel("Fit To Window");
      fitToWindow.addItemListener(this);
      fileMenu.setLabel("File");
      newickOutput.setLabel("Newick Format");
      newickOutput.addActionListener(this);

    add(scrollPane, BorderLayout.CENTER);
      jMenuBar1.add(fileMenu);
      jMenuBar1.add(jMenu2);
      jMenu2.add(fitToWindow);
      jMenu2.add(fontSize);
      jMenu2.add(distanceMenu);
      jMenu2.add(bootstrapMenu);
      jMenu2.add(placeholdersMenu);
    fileMenu.add(newickOutput);
  }

}