/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2007 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;

////////////////////////////////////////////
// This does nothing at all at the moment!!!!!!!!!!
// AW 15th Dec 2004
/////////////////////////////////////////
public class Consensus
{
  int[] mask;
  double threshold;
  String maskstr;

  public Consensus(String mask, double threshold)
  {
    // this.id = id;
    //    this.mask = mask;
    this.maskstr = mask;
    setMask(mask);
    this.threshold = threshold;
  }

  public void setMask(String s)
  {
    this.mask = setNums(s);

    //   for (int i=0; i < mask.length; i++) {
    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
    // }
  }

  public boolean isConserved(int[][] cons2, int col, int size)
  {
    int tot = 0;

    for (int i = 0; i < mask.length; i++)
    {
      tot += cons2[col][mask[i]];
    }

    if ( (double) tot > ( (threshold * size) / 100))
    {
      return true;
    }

    return false;
  }

  int[] setNums(String s)
  {
    int[] out = new int[s.length()];
    int i = 0;

    while (i < s.length())
    {
      out[i] = ResidueProperties.aaIndex[s.charAt(i)];
      i++;
    }

    return out;
  }
}