/* Copyright (c) 2012 Guillaume Collet
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE. 
 */

#ifndef __SCORING_MATRIX_H__
#define __SCORING_MATRIX_H__

#include <string>

using namespace std;

class ScoringMatrix
{
protected:
	string alphabet;
	float ** matrix;
  bool is_set;
	float **norm_matrix;  /**< Normalized vector of each amino acid type */
	float max;
	float min;
	
public:
	ScoringMatrix(string fname);
	virtual ~ScoringMatrix();
	int			getAlphabetSize(){return (int) alphabet.size();};
	string	getAlphabet(){return alphabet;};
	float   getMax(){return max;};
	float		getMin(){return min;};
	int			index(char aa);
	float		score(char aa1, char aa2);
	float		normScore(char aa1, char aa2);
	bool		isSet(){return is_set;};
	
};

#endif