/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 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.datamodel.*;

import jalview.schemes.*;

import java.awt.*;

/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class SequenceRenderer
{
    AlignViewport av;
    FontMetrics fm;
    boolean renderGaps = true;
    SequenceGroup currentSequenceGroup = null;
    SequenceGroup[] allGroups = null;
    Color resBoxColour;
    Graphics graphics;
    boolean monospacedFont;
    boolean forOverview = false;

    /**
     * Creates a new SequenceRenderer object.
     *
     * @param av DOCUMENT ME!
     */
    public SequenceRenderer(AlignViewport av)
    {
        this.av = av;
    }

    /**
     * DOCUMENT ME!
     *
     * @param b DOCUMENT ME!
     */
    public void prepare(Graphics g, boolean renderGaps)
    {
        graphics = g;
        fm = g.getFontMetrics();

        // If EPS graphics, stringWidth will be a double, not an int
        double dwidth = fm.getStringBounds("M", g).getWidth();

        monospacedFont =
               (dwidth == fm.getStringBounds("|",g).getWidth()
               && (float)av.charWidth == dwidth);

        this.renderGaps = renderGaps;
    }


    public Color getResidueBoxColour(SequenceI seq, int i)
    {
      allGroups = av.alignment.findAllGroups(seq);

      if (inCurrentSequenceGroup(i))
      {
        if (currentSequenceGroup.getDisplayBoxes())
        {
          getBoxColour(currentSequenceGroup.cs, seq, i);
        }
      }
      else if (av.getShowBoxes())
      {
          getBoxColour(av.globalColourScheme, seq, i);
      }

      return resBoxColour;
    }


    /**
     * DOCUMENT ME!
     *
     * @param cs DOCUMENT ME!
     * @param seq DOCUMENT ME!
     * @param i DOCUMENT ME!
     */
    void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
    {
        if (cs != null)
        {
            resBoxColour = cs.findColour(seq.getCharAt(i), i);
        }
        else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
        {
            resBoxColour = Color.lightGray;
        }
        else
        {
          resBoxColour = Color.white;
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param g DOCUMENT ME!
     * @param seq DOCUMENT ME!
     * @param sg DOCUMENT ME!
     * @param start DOCUMENT ME!
     * @param end DOCUMENT ME!
     * @param x1 DOCUMENT ME!
     * @param y1 DOCUMENT ME!
     * @param width DOCUMENT ME!
     * @param height DOCUMENT ME!
     */
    public void drawSequence(SequenceI seq, SequenceGroup[] sg,
        int start, int end, int y1)
    {
        allGroups = sg;

        drawBoxes(seq, start, end, y1);

        if (av.validCharWidth)
          drawText(seq, start, end, y1);
    }

    /**
     * DOCUMENT ME!
     *
     * @param seq DOCUMENT ME!
     * @param start DOCUMENT ME!
     * @param end DOCUMENT ME!
     * @param x1 DOCUMENT ME!
     * @param y1 DOCUMENT ME!
     * @param width DOCUMENT ME!
     * @param height DOCUMENT ME!
     */
    public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
    {
      int i = start;
      int length = seq.getLength();

      int curStart = -1;
      int curWidth = av.charWidth;

      Color tempColour = null;

      while (i <= end)
      {
        resBoxColour = Color.white;

        if (i < length)
        {
          if (inCurrentSequenceGroup(i))
          {
            if (currentSequenceGroup.getDisplayBoxes())
            {
              getBoxColour(currentSequenceGroup.cs, seq, i);
            }
          }
          else if (av.getShowBoxes())
          {
            getBoxColour(av.globalColourScheme, seq, i);
          }

        }

          if (resBoxColour != tempColour)
          {
              if (tempColour != null)
              {
                  graphics.fillRect( av.charWidth * (curStart - start), y1,
                      curWidth, av.charHeight);
              }

              graphics.setColor(resBoxColour);

              curStart = i;
              curWidth = av.charWidth;
              tempColour = resBoxColour;
          }
          else
          {
              curWidth += av.charWidth;
          }

          i++;
      }

      graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
          av.charHeight);

    }

    /**
     * DOCUMENT ME!
     *
     * @param seq DOCUMENT ME!
     * @param start DOCUMENT ME!
     * @param end DOCUMENT ME!
     * @param x1 DOCUMENT ME!
     * @param y1 DOCUMENT ME!
     * @param width DOCUMENT ME!
     * @param height DOCUMENT ME!
     */
    public void drawText(SequenceI seq, int start, int end, int y1)
    {
      y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
      int charOffset = 0;
      char s;

        if(end+1>=seq.getLength())
          end = seq.getLength()-1;
        graphics.setColor(av.textColour);


        if(monospacedFont
           && av.showText
           && allGroups.length==0
           && !av.getColourText()
           && av.thresholdTextColour==0)
        {
          if (av.renderGaps)
            graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
          else
         {
           char gap = av.getGapCharacter();
           graphics.drawString( seq.getSequenceAsString(start, end+1).replace(gap, ' '), 0, y1);
         }
        }
        else
        {
          boolean getboxColour = false;
          for (int i = start; i <= end; i++)
          {
            graphics.setColor(av.textColour);
            getboxColour = false;
            s = seq.getCharAt(i);
            if (!renderGaps && jalview.util.Comparison.isGap(s))
            {
              continue;
            }

            if (inCurrentSequenceGroup(i))
            {
              if (!currentSequenceGroup.getDisplayText())
              {
                continue;
              }

              if (currentSequenceGroup.thresholdTextColour > 0
                  || currentSequenceGroup.getColourText())
              {
                getboxColour = true;
                getBoxColour(currentSequenceGroup.cs, seq, i);

                if (currentSequenceGroup.getColourText())
                  graphics.setColor(resBoxColour.darker());

                if (currentSequenceGroup.thresholdTextColour > 0)
                {
                  if (resBoxColour.getRed() +
                      resBoxColour.getBlue() +
                      resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
                    graphics.setColor(currentSequenceGroup.textColour2);
                }
              }
              else
                  graphics.setColor(currentSequenceGroup.textColour);

            }
            else
            {
              if (!av.getShowText())
              {
                continue;
              }

              if (av.getColourText())
              {
                getboxColour = true;
                getBoxColour(av.globalColourScheme, seq, i);

                if (av.getShowBoxes())
                {
                  graphics.setColor(resBoxColour.darker());
                }
                else
                {
                  graphics.setColor(resBoxColour);
                }
              }

              if (av.thresholdTextColour > 0)
              {
                if (!getboxColour)
                  getBoxColour(av.globalColourScheme, seq, i);

                if (resBoxColour.getRed() +
                    resBoxColour.getBlue() +
                    resBoxColour.getGreen() < av.thresholdTextColour)
                  graphics.setColor(av.textColour2);
              }

            }



          charOffset = (av.charWidth - fm.charWidth(s)) / 2;
          graphics.drawString(String.valueOf(s),
                              charOffset + av.charWidth * (i - start),
                              y1);

          }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param res DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    boolean inCurrentSequenceGroup(int res)
    {
        if (allGroups == null)
        {
            return false;
        }

        for (int i = 0; i < allGroups.length; i++)
        {
            if ((allGroups[i].getStartRes() <= res) &&
                    (allGroups[i].getEndRes() >= res))
            {
                currentSequenceGroup = allGroups[i];

                return true;
            }
        }

        return false;
    }

    /**
     * DOCUMENT ME!
     *
     * @param seq DOCUMENT ME!
     * @param start DOCUMENT ME!
     * @param end DOCUMENT ME!
     * @param x1 DOCUMENT ME!
     * @param y1 DOCUMENT ME!
     * @param width DOCUMENT ME!
     * @param height DOCUMENT ME!
     */
    public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
    {
        int pady = av.charHeight / 5;
        int charOffset = 0;
        graphics.setColor(Color.BLACK);
        graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
        graphics.setColor(Color.white);

        char s = '~';

        // Need to find the sequence position here.
        if(av.validCharWidth)
        {
          for (int i = start; i <= end; i++)
          {
            if (i < seq.getLength())
            {
              s = seq.getCharAt(i);
            }

            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
            graphics.drawString(String.valueOf(s),
                                charOffset + x1 + (av.charWidth * (i - start)),
                                (y1 + av.charHeight) - pady);
          }
        }
    }

    public void drawCursor(SequenceI seq, int res, int x1, int y1)
    {
      int pady = av.charHeight / 5;
      int charOffset = 0;
      graphics.setColor(Color.black);
      graphics.fillRect(x1, y1, av.charWidth, av.charHeight);

      if(av.validCharWidth)
      {
        graphics.setColor(Color.white);

        char s = seq.getCharAt(res);

        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
        graphics.drawString(String.valueOf(s),
                            charOffset + x1,
                            (y1 + av.charHeight) - pady);
      }

    }
}