/* Jalview - a java multiple alignment editor
 * Copyright (C) 1998  Michele Clamp
 *
 * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 */

package jalview.schemes;
import java.awt.*;
import jalview.gui.*;
import jalview.datamodel.*;
import jalview.analysis.*;

public class ConservationColourScheme extends ResidueColourScheme {
  public Conservation conserve;
  boolean byResidue = true;
  public ColourSchemeI cs;
  public int inc = 30;
  int colourThreshold =  7;

  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
  {
    super();
    conserve = cons;
    cs = oldcs;
  }

  public void setColours(DrawableSequence seq, int j) {
    Color c = Color.white;
    String s = seq.getSequence().substring(j,j+1);

      if (colourThreshold > 0 && conserve.getConsSequence() != null) {
        if (fullConservation(j)) {
          if (byResidue) {
            c = findColour(seq,s,j);
           } else {
             c = Color.red;
           }
        } else {
          if (byResidue) {

            int tmp = 10;
            int t = Integer.parseInt(conserve.getConsSequence().getSequence().substring(j,j+1));
            c = findColour(seq,s,j);

             while (tmp >= t) {
              //      c = c.darker();
              c = lighter(c,inc);
               tmp--;
             }
          } else {
          c = Color.yellow;
          }
        }
      }

      seq.setColor(c);
  }
   public Color findColour(String s, int i, java.util.Vector whatever)
   {
     Color c = null;
     if (colourThreshold > 0 && conserve.getConsSequence() != null)
     {
       if (fullConservation(i)) {
         if (byResidue) {
           c = findColour(null,s,i);
          } else {
            c = Color.red;
          }
       } else {
         if (byResidue) {

           int tmp = 10;
           int t = 0;
           if( !jalview.util.Comparison.isGap( conserve.getConsSequence().getSequence().charAt(i) ))
               t=Integer.parseInt(conserve.getConsSequence().getSequence().substring(i,i+1));

           c = findColour(null,s,i);

            while (tmp >= t) {
             //      c = c.darker();
             c = lighter(c,inc);
              tmp--;
            }
         } else {
         c = Color.yellow;
         }
       }
     }
     return c;
   }

  public Color findColour(DrawableSequence seq, String s, int j) {
    if(cs!=null)
      return cs.findColour( s, -1, null);
    else
      return Color.white;
  }
  public boolean fullConservation(int j) {
    String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
    if (tmp.equals("*")) return true; else return false;
  }
  public boolean aboveThreshold(DrawableSequence seq, int j, int threshold) {
    String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);

    if (Integer.parseInt(tmp) >= threshold || tmp.equals("*")) {
      return true;
    } else {
      return false;
    }
  }

  public Color lighter(Color c, int inc) {
    int red = c.getRed();
    int blue = c.getBlue();
    int green = c.getGreen();

    if (red < 255-inc) { red = red +inc;} else {red = 255;}
    if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}
    if (green < 255-inc) { green = green +inc;} else {green = 255;}

    return new Color(red,green,blue);
  }

}