/*
 * 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.io.*;
import java.util.*;
import javax.imageio.*;

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

import org.jibble.epsgraphics.*;
import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;

public class TreePanel
    extends GTreePanel
{
  SequenceI[] seq;
  String type;
  String pwtype;
  AlignViewport av;
  int start;
  int end;
  TreeCanvas treeCanvas;
  NJTree tree;

  public TreePanel(AlignViewport av, Vector seqVector, String type,
                   String pwtype, int s, int e)
  {
    super();

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

    start = s;
    end = e;

    String longestName = "";
    seq = new Sequence[seqVector.size()];

    for (int i = 0; i < seqVector.size(); i++)
    {
      seq[i] = (Sequence) seqVector.elementAt(i);

      if (seq[i].getName().length() > longestName.length())
      {
        longestName = seq[i].getName();
      }
    }

    tree = new NJTree(seq, type, pwtype, start, end);

    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
    treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
    setViewStateFromTreeCanvas(treeCanvas);
    tree.reCount(tree.getTopNode());
    tree.findHeight(tree.getTopNode());
    scrollPane.setViewportView(treeCanvas);
  }

  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
                   String type, String pwtype)
  {
    super();

    // These are probably only  arbitrary strings reflecting source of tree
    this.type = type;
    this.pwtype = pwtype;

    start = 0;
    end = seqVector.size();

    String longestName = "";
    seq = new Sequence[seqVector.size()];

    for (int i = 0; i < seqVector.size(); i++)
    {
      seq[i] = (Sequence) seqVector.elementAt(i);
    }

    // This constructor matches sequence names to treenodes and sets up the tree layouts.
    tree = new NJTree(seq, newtree);

    // Now have to calculate longest name based on the leaves
    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
    boolean has_placeholders = false;

    for (int i = 0; i < leaves.size(); i++)
    {
      SequenceNode lf = (SequenceNode) leaves.elementAt(i);

      if (lf.isPlaceholder())
      {
        has_placeholders = true;
      }

      if (longestName.length() < ( (Sequence) lf.element()).getName()
          .length())
      {
        longestName = TreeCanvas.PLACEHOLDER +
            ( (Sequence) lf.element()).getName();
      }
    }

    tree.reCount(tree.getTopNode());
    tree.findHeight(tree.getTopNode());

    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
    treeCanvas.setShowBootstrap(newtree.HasBootstrap());
    treeCanvas.setShowDistances(newtree.HasDistances());
    scrollPane.setViewportView(treeCanvas);
    treeCanvas.setMarkPlaceholders(has_placeholders);
    setViewStateFromTreeCanvas(treeCanvas);

    // JBPNote TODO: preference for always marking placeholders in new associated tree
  }

  public NJTree getTree()
  {
    return tree;
  }

  private void setViewStateFromTreeCanvas(TreeCanvas tree)
  {
    // update view menu state from treeCanvas render state
    distanceMenu.setSelected(tree.showDistances);
    bootstrapMenu.setSelected(tree.showBootstrap);
    placeholdersMenu.setSelected(tree.markPlaceholders);
  }

  private void setTreeCanvasFromViewState(TreeCanvas tree)
  {
    // update view menu state from treeCanvas render state
    tree.showDistances = distanceMenu.isSelected();
    tree.showBootstrap = bootstrapMenu.isSelected();
    tree.markPlaceholders = placeholdersMenu.isSelected();
  }

  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(false, true));
  }

  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(false, true); // distances only
        java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
            FileWriter(
                choice));
        out.println(output);
        out.close();
      }
      catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }
  }

  protected void printMenu_actionPerformed(ActionEvent e)
  {
    //Putting in a thread avoids Swing painting problems
    treeCanvas.startPrinting();
  }

  protected void fitToWindow_actionPerformed(ActionEvent e)
  {
    treeCanvas.fitToWindow = fitToWindow.isSelected();
    repaint();
  }

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

    String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
                                               1);

    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
        "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,
        null,
        new String[]
        {
        "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"
    }, "Font Size - " + size);

    if (selection != null)
    {
      fontSize.setText("Font Size - " + selection);

      int i = Integer.parseInt(selection.toString());
      treeCanvas.setFontSize(i);
    }

    scrollPane.setViewportView(treeCanvas);
  }

  protected void distanceMenu_actionPerformed(ActionEvent e)
  {
    treeCanvas.setShowDistances(distanceMenu.isSelected());
  }

  protected void bootstrapMenu_actionPerformed(ActionEvent e)
  {
    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
  }

  protected void placeholdersMenu_actionPerformed(ActionEvent e)
  {
    treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
  }

  protected void epsTree_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[]
          {"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);

      treeCanvas.draw(pg, width, height);

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

  protected 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();
    }
  }
}