/*
* $Id: Matrix.java,v 1.2 2006/01/18 20:16:37 ahmed Exp $
*
* 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 jaligner.matrix;
import java.io.Serializable;
/**
* Scoring matrix.
*
* @author Ahmed Moustafa (ahmed@users.sf.net)
*/
public class Matrix implements Serializable {
/**
*
*/
private static final long serialVersionUID = 3833742170619524400L;
/**
* The size of the scoring matrix. It is the number of the characters in the
* ASCII table. It is more than the 20 amino acids just to save the
* processing time of the mapping.
*/
public static final int SIZE = 127;
/**
* Matrix id (or name)
*/
private final String id;
/**
* Scores
*/
private final float[][] scores;
public Matrix(String id, float[][] scores) {
this.id = id;
this.scores = scores;
}
/**
* @return Returns the id.
*/
public String getId() {
return this.id;
}
/**
* @return Returns the scores.
*/
public float[][] getScores() {
return this.scores;
}
/**
*
* @param a
* @param b
* @return score
*/
public float getScore(char a, char b) {
return this.scores[a][b];
}
}