/*
 * 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.schemes;

import java.awt.*;

import jalview.datamodel.*;
import jalview.analysis.AAFrequency;

public class PIDColourScheme
    extends ResidueColourScheme
{
  public Color[] pidColours;
  public float[] thresholds;
  SequenceGroup group;

  public PIDColourScheme()
  {
    this.pidColours = ResidueProperties.pidColours;
    this.thresholds = ResidueProperties.pidThresholds;
  }

  public Color findColour(String s, int j)
  {
    char res = s.charAt(0);
    if ('a' <= res && res <= 'z')
    {
      s = String.valueOf(res -= ('a' - 'A'));
    }

    if (consensus == null
        || j >= consensus.length
        || consensus[j]==null)
    {
      return Color.white;
    }

    if ( (threshold != 0) && !aboveThreshold(s, j))
    {
      return Color.white;
    }

    currentColour = Color.white;

    double sc = 0;

    if(consensus.length<=j)
      return Color.white;

      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
          consensus[j].contains(s))
      {
        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();

        if (!jalview.util.Comparison.isGap(res))
        {
          for (int i = 0; i < thresholds.length; i++)
          {
            if (sc > thresholds[i])
            {
              currentColour = pidColours[i];

              break;
            }
          }
        }
      }

    if(conservationColouring)
         applyConservation(j);

    return currentColour;
  }
}