/*
* 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.awt.*;
import jalview.datamodel.*;
import jalview.analysis.*;


public class SeqCanvas extends Panel
{
    FeatureRenderer fr;
    SequenceRenderer sr;
    Image             img;
    Graphics          gg;
    int               imgWidth;
    int               imgHeight;

    AlignViewport     av;

    boolean showScores = false;
    boolean displaySearch = false;
    int [] searchResults = null;

    int chunkHeight;
    int chunkWidth;

    boolean fastPaint = false;


    public SeqCanvas(AlignViewport av)
    {
	this.av         = av;
       fr = new FeatureRenderer(av);
       sr = new SequenceRenderer(av);
       PaintRefresher.Register(this);

    }

  void drawNorthScale(Graphics g, int startx, int endx,int ypos) {
    int scalestartx = startx - startx % 10 + 10;

    g.setColor(Color.black);

    // NORTH SCALE
    for (int i = scalestartx; i < endx; i += 10)
    {
      String string = String.valueOf(i);
      g.drawString(string, (i - startx - 1) * av.charWidth,
                   ypos - av.charHeight / 2);

      g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,
                 ypos + 2 - av.charHeight / 2,
                 (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);

    }
  }

  void drawWestScale(Graphics g, int startx, int endx, int ypos)
  {
    FontMetrics fm = getFontMetrics(av.getFont());
    ypos+= av.charHeight;
      // EAST SCALE
    for (int i = 0; i < av.alignment.getHeight(); i++)
    {
      SequenceI seq = av.alignment.getSequenceAt(i);
      int index = startx;
      int value = -1;
      while (index < endx)
      {
        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
        {
          index++;
          continue;
        }

        value = av.alignment.getSequenceAt(i).findPosition(index);
        break;
      }
      if(value!=-1)
      {
        int x = LABEL_WEST - fm.stringWidth(value+"");
        g.drawString(value + "", x,  ypos +  i*av.charHeight - av.charHeight/5);
      }
    }
  }

  void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
    ypos+= av.charHeight;
    // EAST SCALE
  for (int i = 0; i < av.alignment.getHeight(); i++)
  {
    SequenceI seq = av.alignment.getSequenceAt(i);
    int index = endx;
    int value = -1;
    while (index > startx)
    {
      if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
      {
        index--;
        continue;
      }

      value = av.alignment.getSequenceAt(i).findPosition(index);
      break;
    }
    if(value!=-1)
       g.drawString(value + "", 0,  ypos +  i*av.charHeight - av.charHeight/5);
  }

}



public void fastPaint(int horizontal, int vertical)
{
    if (horizontal == 0 && vertical == 0 || gg==null)
      return;

    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
                -vertical * av.charHeight);

    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
        transX = 0, transY = 0;
    if (horizontal > 0) // scrollbar pulled right, image to the left
    {
      transX = (er - sr - horizontal) * av.charWidth;
      sr = er - horizontal;
    }
    else if (horizontal < 0)
      er = sr - horizontal;

    else if (vertical > 0) // scroll down
    {
      ss = es - vertical;
      if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time
        ss = av.startSeq;
      else
        transY = imgHeight - vertical * av.charHeight;
    }
    else if (vertical < 0)
    {
      es = ss - vertical;
      if(es > av.endSeq)
        es = av.endSeq;
    }


    gg.translate(transX, transY);

    gg.setColor(Color.white);
    gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);
    drawPanel(gg, sr, er, ss, es, sr, ss, 0);
    gg.translate( -transX, -transY);

    fastPaint = true;
    repaint();

}

/**
 * Definitions of startx and endx (hopefully):
 * SMJS This is what I'm working towards!
 *   startx is the first residue (starting at 0) to display.
 *   endx   is the last residue to display (starting at 0).
 *   starty is the first sequence to display (starting at 0).
 *   endy   is the last sequence to display (starting at 0).
 * NOTE 1: The av limits are set in setFont in this class and
 * in the adjustment listener in SeqPanel when the scrollbars move.
 */
  public void update(Graphics g)
  {
    paint(g);
  }

  public void paint(Graphics g)
  {
    if (fastPaint)
    {
      g.drawImage(img, 0, 0, this);
      fastPaint = false;
      return;
    }

    // this draws the whole of the alignment
      imgWidth  = this.getSize().width;
      imgHeight = this.getSize().height;

      imgWidth -= imgWidth%av.charWidth;
      imgHeight-= imgHeight%av.charHeight;

      if(imgWidth<1 || imgHeight<1)
              return;

      if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this))
      {
        img = createImage(imgWidth, imgHeight);
        gg = img.getGraphics();
        gg.setFont(av.getFont());
      }

      gg.setColor(Color.white);
      gg.fillRect(0,0,imgWidth,imgHeight);

    chunkWidth  =   getWrappedCanvasWidth( getSize().width );
    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;

    av.setChunkHeight(chunkHeight);
    av.setChunkWidth(chunkWidth);


    if (av.getWrapAlignment())
      drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);
    else
      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);

    g.drawImage(img, 0, 0, this);

  }

  int LABEL_WEST, LABEL_EAST;
  public int getWrappedCanvasWidth(int cwidth)
  {
    FontMetrics fm = getFontMetrics(av.getFont());

    LABEL_EAST = 0;
    LABEL_WEST = 0;

    if(av.scaleRightWrapped)
      LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );

    if(av.scaleLeftWrapped)
      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );

    return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
  }

  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
  {
      AlignmentI al = av.getAlignment();

      FontMetrics fm = getFontMetrics(av.getFont());

      int LABEL_EAST = 0;
      if(av.scaleRightWrapped)
        LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );
      int LABEL_WEST = 0;
      if(av.scaleLeftWrapped)
        LABEL_WEST = fm.stringWidth(al.getWidth()+"0");


      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;

      av.endRes = av.startRes + cWidth;

      int  endx   = startRes+cWidth-1;
      int  ypos  = 2*av.charHeight;

      while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )
      {
        g.setColor(Color.black);

        if(av.scaleLeftWrapped)
          drawWestScale(g, startRes, endx, ypos);

        if(av.scaleRightWrapped)
        {
          g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);
          drawEastScale(g, startRes, endx, ypos);
          g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);
        }

        g.translate(LABEL_WEST,0);
        if(av.scaleAboveWrapped)
          drawNorthScale(g, startRes, endx, ypos);


        // When printing we have an extra clipped region,
        // the Printable page which we need to account for here
        Shape clip = g.getClip();
        if(clip==null)
          g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);
        else
          g.setClip(0,
                    (int)clip.getBounds().y,
                    cWidth*av.charWidth,
                    (int)clip.getBounds().height
                    );

        drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
        g.setClip(clip);
        g.translate(-LABEL_WEST,0);

        ypos += cHeight;
        startRes += cWidth;
        endx = startRes + cWidth - 1;

        if (endx > al.getWidth())
          endx = al.getWidth();
      }

  }


  synchronized public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {

    g.setFont(av.getFont());
    sr.renderGaps(av.renderGaps);

    SequenceI nextSeq;

    /// First draw the sequences
    /////////////////////////////
    for (int i = y1 ; i < y2 ;i++)
    {
     nextSeq = av.alignment.getSequenceAt(i);

     sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,
                 (x1 - startx) * av.charWidth,
                 offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
                 av.charWidth,av.charHeight);

     if(av.showSequenceFeatures)
     {
       fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,
                       (x1 - startx) * av.charWidth,
                       offset +
                       AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
                       av.charWidth, av.charHeight);
     }
    }
    //
    /////////////////////////////////////

    // Now outline any areas if necessary
    /////////////////////////////////////
    SequenceGroup group = av.getSelectionGroup();
    java.util.Vector groups = av.alignment.getGroups();

    int sx = -1, sy = -1, ex = -1;
    int groupIndex = -1;
    if (group == null && groups.size() > 0)
    {
      group = (SequenceGroup) groups.elementAt(0);
      groupIndex = 0;
    }

    if (group != null)
      do
      {
        int oldY = -1;
        int i = 0;
        boolean inGroup = false;
        int top=-1, bottom =-1;
        for (i = y1; i < y2; i++)
        {
          sx = (group.getStartRes() - startx) * av.charWidth;
          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;

          if (sx < getSize().width
              && ex > 0
              && group.sequences.contains(av.alignment.getSequenceAt(i)))
          {
            if (bottom == -1 && (i==av.alignment.getHeight()-1 ||
                !group.sequences.contains(av.alignment.getSequenceAt(i + 1))))
              bottom = sy + av.charHeight ;

            if (!inGroup)
            {
              if (top == -1 && i==0 ||
                  !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
                top = sy;


              oldY = sy;
              inGroup = true;
              if (group == av.getSelectionGroup())
              {
                    g.setColor(new Color(255,0,0));
              }
              else
              {
                    g.setColor(group.getOutlineColour());
              }
            }
          }
          else
          {
            if (inGroup)
            {
              g.drawLine(sx, oldY, sx, sy );
              g.drawLine(sx+ex, oldY, sx+ex, sy );

              if (top != -1)
              {
                g.drawLine(sx, top, sx + ex, top);
                top =-1;
              }
              if (bottom != -1)
              {
                g.drawLine(sx, bottom, sx + ex, bottom);
                bottom = -1;
              }


              inGroup = false;
            }
          }
        }

        if (inGroup)
        {

          if(top!=-1)
          {
            g.drawLine(sx, top, sx + ex, top);
            top =-1;
          }
          if(bottom!=-1)
           {
             g.drawLine(sx, bottom-1, sx + ex, bottom-1);
             bottom = -1;

           }
          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
          g.drawLine(sx, oldY, sx, sy );
          g.drawLine(sx+ex, oldY, sx+ex, sy );
          inGroup = false;
        }
        groupIndex++;
        if (groupIndex >= groups.size())
          break;

        group = (SequenceGroup) groups.elementAt(groupIndex);

      }
      while (groupIndex < groups.size());


    /// Highlight search Results once all sequences have been drawn
    //////////////////////////////////////////////////////////
    if(displaySearch)
    {
      for(int r=0; r<searchResults.length; r+=3)
      {
        int searchSeq = searchResults[r];

        if (searchSeq >= y1 && searchSeq < y2)
        {
          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);

          int searchStart = seq.findIndex( searchResults[r+1] )-1;
          int searchEnd =  seq.findIndex(  searchResults[r+2] )-1;

          SequenceRenderer ssr = (SequenceRenderer) sr;
          if(searchStart<x1)
            searchStart = x1;
          if(searchEnd > x2)
            searchEnd = x2;

          ssr.drawHighlightedText(seq,
                                  searchStart,
                                  searchEnd,
                                  (searchStart - startx) * av.charWidth,
                                  offset +
                                  AlignmentUtil.getPixelHeight(starty, searchSeq,
              av.charHeight),
                                  av.charWidth,
                                  av.charHeight);
        }
      }
    }

  }



  public void highlightSearchResults(int [] results)
  {
    // results are in the order sequence, startRes, endRes
    if(results==null)
      displaySearch = false;
    else
      displaySearch = true;

    searchResults = results;

    repaint();
  }


}