package jalview.gui;

import jalview.datamodel.*;
import jalview.analysis.*;
import jalview.jbgui.GTreePanel;
import jalview.io.*;
import java.awt.event.*;
import java.util.*;
import java.io.*;
import javax.swing.*;
import java.awt.*;
import java.awt.image.*;
import org.jibble.epsgraphics.*;
import javax.imageio.*;



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

  public NJTree getTree()
  {
    return 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);

  }
  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 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 void textbox_actionPerformed(ActionEvent e)
    {
      CutAndPasteTransfer cap = new CutAndPasteTransfer();
      JInternalFrame frame = new JInternalFrame();
      frame.setContentPane(cap);

      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(frame,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(), 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(), 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();
    }
  }

}