/*
* 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 jalview.analysis.*;
import jalview.datamodel.*;
import jalview.util.*;
import jalview.schemes.*;
import javax.swing.*;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import java.awt.print.*;

public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable
{
  NJTree tree;
  JScrollPane scrollPane;
  AlignViewport av;
  public static final String PLACEHOLDER=" * ";
  Font font;
  int  fontSize = 12;

  boolean fitToWindow = true;
  boolean showDistances = false;
  boolean showBootstrap = false;
  boolean markPlaceholders = false;

  int offx = 20;
  int offy = 20;

  float threshold;

  String longestName;
  int labelLength=-1;

  //RubberbandRectangle rubberband;

  Vector    listeners;

  Hashtable nameHash = new Hashtable();
  Hashtable nodeHash = new Hashtable();

  public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, String label)
  {
    this.av = av;
    this.tree     = tree;
    scrollPane = scroller;
    addMouseListener(this);
    tree.findHeight(tree.getTopNode());
    longestName = label;

    PaintRefresher.Register(this);
  }
  public void TreeSelectionChanged(Sequence sequence)
 {
    SequenceGroup selected = av.getSelectionGroup();
    if(selected == null)
    {
      selected = new SequenceGroup();
      av.setSelectionGroup(selected);
    }

    selected.setEndRes(av.alignment.getWidth());
    selected.addOrRemove(sequence);


    PaintRefresher.Refresh(this);
    repaint();
 }



  public void setTree(NJTree tree) {
    this.tree = tree;
    tree.findHeight(tree.getTopNode());
  }

    public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
    if (node == null) {
      return;
    }

    if (node.left() == null && node.right() == null) {
      // Drawing leaf node

      float height = node.height;
      float dist   = node.dist;

      int xstart = (int)((height-dist)*scale) + offx;
      int xend =   (int)(height*scale)        + offx;

      int ypos = (int)(node.ycount * chunk) + offy;

      if (node.element() instanceof SequenceI)
      {
       if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() == Color.white)
       {
         g.setColor(Color.black);
       }
       else
        g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().
                   darker());

      }
      else
          g.setColor(Color.black);


      // Draw horizontal line
      g.drawLine(xstart,ypos,xend,ypos);

      String nodeLabel = "";
      if (showDistances && node.dist > 0) {
        nodeLabel = new Format("%5.2f").form(node.dist);
      }
      if (showBootstrap) {
        if (showDistances) {
          nodeLabel = nodeLabel + " : ";
        }
        nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
      }
      if (! nodeLabel.equals("")) {
      g.drawString(nodeLabel,xstart,ypos - 10);
      }

      String name    = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER+node.getName()) : node.getName();
      FontMetrics fm = g.getFontMetrics(font);
      int charWidth  = fm.stringWidth(name) + 3;
      int charHeight = fm.getHeight();

      Rectangle rect = new Rectangle(xend+20,ypos-charHeight,
                                     charWidth,charHeight);

      nameHash.put((SequenceI)node.element(),rect);

      // Colour selected leaves differently
      SequenceGroup selected = av.getSelectionGroup();
      if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {
        g.setColor(Color.gray);

        g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);
        g.setColor(Color.white);
      }
      g.drawString(name,xend+10,ypos);
      g.setColor(Color.black);
    } else {
      drawNode(g,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
      drawNode(g,(SequenceNode)node.right(),chunk,scale,width,offx,offy);

      float height = node.height;
      float dist   = node.dist;

      int xstart = (int)((height-dist)*scale) + offx;
      int xend   = (int)(height       *scale) + offx;
      int ypos   = (int)(node.ycount  *chunk) + offy;

      g.setColor(((SequenceNode)node).color.darker());

      // Draw horizontal line
      g.drawLine(xstart,ypos,xend,ypos);
      g.fillRect(xend-2, ypos-2, 4,4);

      int ystart = (int)(((SequenceNode)node.left()) .ycount * chunk) + offy;
      int yend   = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;

      Rectangle pos = new Rectangle(xend-2,ypos-2,5,5);
      nodeHash.put(node,pos);

      g.drawLine((int)(height*scale) + offx, ystart,
                 (int)(height*scale) + offx, yend);

      if (showDistances && node.dist > 0) {
        g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
      }

    }
  }
  public Object findElement(int x, int y) {
       Enumeration keys = nameHash.keys();

    while (keys.hasMoreElements()) {
            Object ob = keys.nextElement();
            Rectangle rect = (Rectangle)nameHash.get(ob);

            if (x >= rect.x && x <= (rect.x + rect.width) &&
              y >= rect.y && y <= (rect.y + rect.height)) {
              return ob;
            }
  }
  keys = nodeHash.keys();

    while (keys.hasMoreElements()) {
            Object ob = keys.nextElement();
            Rectangle rect = (Rectangle)nodeHash.get(ob);

            if (x >= rect.x && x <= (rect.x + rect.width) &&
              y >= rect.y && y <= (rect.y + rect.height)) {
              return ob;
            }
    }
      return null;

  }

  public void pickNodes(Rectangle pickBox) {
    int width  = getWidth();
    int height = getHeight();

    SequenceNode top = tree.getTopNode();

    float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()
;
    if (top.count == 0) {
      top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
    }
    float chunk = (float)(height-offy*2)/top.count;

    pickNode(pickBox,top,chunk,wscale,width,offx,offy);
  }

  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
    if (node == null) {
      return;
    }

    if (node.left() == null && node.right() == null) {
      float height = node.height;
      float dist   = node.dist;

      int xstart = (int)((height-dist)*scale) + offx;
      int xend   = (int)(height*scale) + offx;

      int ypos = (int)(node.ycount * chunk) + offy;

      if (pickBox.contains(new Point(xend,ypos))) {
        if (node.element() instanceof SequenceI) {
          SequenceI seq = (SequenceI)node.element();
          SequenceGroup sg = av.getSelectionGroup();
          if(sg!=null)
            sg.addOrRemove(seq);
        }
      }
    } else {
      pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
      pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
    }
  }

  public void setColor(SequenceNode node, Color c)
  {
    if (node == null)
      return;

    if (node.left() == null && node.right() == null)
    {
      node.color = c;

      if (node.element() instanceof SequenceI)
          ((SequenceI)node.element()).setColor(c);
    } else
    {
      node.color = c;
      setColor((SequenceNode)node.left(),c);
      setColor((SequenceNode)node.right(),c);
    }
  }

  void startPrinting()
  {
    Thread thread = new Thread(this);
    thread.start();
  }

  // put printing in a thread to avoid painting problems
  public void run()
  {
    PrinterJob printJob = PrinterJob.getPrinterJob();
    PageFormat pf = printJob.pageDialog(printJob.defaultPage());

    printJob.setPrintable(this, pf);
    if (printJob.printDialog())
    {
      try
      {
        printJob.print();
      }
      catch (Exception PrintException)
      {
        PrintException.printStackTrace();
      }
    }
  }


  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
  {

    pg.setFont(font);
    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
    int pwidth = (int) pf.getImageableWidth();
    int pheight = (int) pf.getImageableHeight();

    int noPages = getHeight() / pheight;
    if(pi>noPages)
      return Printable.NO_SUCH_PAGE;


    if (pwidth > getWidth())
        pwidth = getWidth();

    if(fitToWindow)
    {
      if (pheight > getHeight())
        pheight = getHeight();

      noPages = 0;
    }
    else
    {

        FontMetrics fm = pg.getFontMetrics(font);
        int height = fm.getHeight() * nameHash.size();
        pg.translate(0, -pi*pheight  );
        pg.setClip(0,pi*pheight, pwidth,pi*pheight + pheight);
       // translate number of pages,
       // height is screen size as this is the
       // non overlapping text size
        pheight = height;
    }

    draw(pg, pwidth, pheight);

    return Printable.PAGE_EXISTS;

  }

  public void paintComponent(Graphics g)
  {

    font = new Font("Verdana",Font.PLAIN,fontSize);
    g.setFont(font);

    FontMetrics fm = g.getFontMetrics(font);

    if(nameHash.size()==0)
      repaint();


    if( fitToWindow || (!fitToWindow && scrollPane.getHeight() > fm.getHeight() * nameHash.size()+offy ) )
     {
         draw(g,scrollPane.getWidth(),scrollPane.getHeight());
         setPreferredSize(null);
     }
    else
     {
         setPreferredSize(new Dimension(scrollPane.getWidth(), fm.getHeight() * nameHash.size()));
         draw( g,scrollPane.getWidth(), fm.getHeight() * nameHash.size());
     }

    scrollPane.revalidate();
  }
    public int getFontSize() {
        return fontSize;
    }
    public void setFontSize(int fontSize) {
        this.fontSize = fontSize;
        repaint();
    }
  public void draw(Graphics g1, int width, int height) {

      Graphics2D g2 = (Graphics2D)g1;
      g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
      g2.setColor(Color.white);
      g2.fillRect(0,0,width,height);


      labelLength = g2.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar

      float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();

      SequenceNode top = tree.getTopNode();

      if (top.count == 0) {
          top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
      }
      float chunk = (float)(height-offy*2)/top.count ;

      drawNode(g2,tree.getTopNode(),chunk,wscale,width,offx,offy);

      if (threshold != 0)
      {
        if(av.getCurrentTree() == tree)
          g2.setColor(Color.red);
        else
          g2.setColor(Color.gray);

          int x = (int)(    threshold * (float)(getWidth()-labelLength - 2*offx) +offx   ) ;

          g2.drawLine(x,0,x,getHeight());
      }

  }

  public void mouseReleased(MouseEvent e) { }
  public void mouseEntered(MouseEvent e) { }
  public void mouseExited(MouseEvent e) { }
  public void mouseClicked(MouseEvent e) {
  }

  public void mousePressed(MouseEvent e) {

      av.setCurrentTree(tree);

      int x = e.getX();
      int y = e.getY();

      Object ob = findElement(x,y);

      if (ob instanceof SequenceI)
      {
          TreeSelectionChanged((Sequence)ob);
          repaint();
          return;

      } else if (ob instanceof SequenceNode) {
          SequenceNode tmpnode = (SequenceNode)ob;
          tree.swapNodes(tmpnode);
          tree.reCount(tree.getTopNode());
          tree.findHeight(tree.getTopNode());
      } else {
          // Find threshold

          if (tree.getMaxHeight() != 0) {
              threshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);

              tree.getGroups().removeAllElements();
              tree.groupNodes(tree.getTopNode(),threshold);
              setColor(tree.getTopNode(),Color.black);

              av.setSelectionGroup(null);
              av.alignment.deleteAllGroups();

              for (int i=0; i < tree.getGroups().size(); i++)
              {

                  Color col = new Color((int)(Math.random()*255),
                                        (int)(Math.random()*255),
                                        (int)(Math.random()*255));
                  setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());

                  Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
                  SequenceGroup sg = null;
                  for (int j = 0; j < l.size(); j++)
                  {
                    SequenceNode sn = (SequenceNode) l.elementAt(j);
                    if(sg==null)
                       sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());

                    sg.addSequence( (Sequence) sn.element());
                  }

                  if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
                  {
                    ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();
                    Conservation c = new Conservation("Group",
                                                      ResidueProperties.propHash, 3,
                                                      sg.sequences, sg.getStartRes(),
                                                      sg.getEndRes());

                    c.calculate();
                    c.verdict(false, av.ConsPercGaps);
                    ccs = new ConservationColourScheme(c, ccs.cs);

                    sg.cs = ccs;

                  }



                  av.alignment.addGroup(sg);

              }
          }
      }

      PaintRefresher.Refresh(this);
      repaint();

  }

    public void setShowDistances(boolean state) {
        this.showDistances = state;
        repaint();
    }

    public void setShowBootstrap(boolean state) {
      this.showBootstrap = state;
      repaint();
    }
    public void setMarkPlaceholders(boolean state) {
            this.markPlaceholders = state;
            repaint();
    }

}