/**
 * Copyright 2015 Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *     http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package com.salsaw.salsa.algorithm;

/**
 * It represent the substitution matrix.
 * The role is to return the value of m(α;β) using method score. 
 * 
 * <p>Note: inside the matrix is represented by an array</p>
 * 
 * @author Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 *
 */
public final class SubstitutionMatrix {

}

/**
 * Copyright 2015 Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *     http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package com.salsaw.salsa.algorithm;

import com.salsaw.salsa.algorithm.exceptions.SALSAException;

/**
 * It represent the substitution matrix. The role is to return the value of
 * m(α;β) using method score.
 * 
 * <p>
 * Note: inside the matrix is represented by an array
 * </p>
 * 
 * @author Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 *
 */
public final class SubstitutionMatrix {

	// FIELDS
	private final int alphabetLength;
	/**
	 * GAP extension penalty
	 */
	private final float GEP;

	private final Alphabet alphabet;

	private final int[] matrix;

	// CONSTRUCTOR

	// GET/SET
	public final Alphabet getAlphabet() {
		return this.alphabet;
	}

	public SubstitutionMatrix(String filePath, int alphabetLength, float gep)
			throws SALSAException {
		this.matrix = new int[alphabetLength * alphabetLength];
		this.alphabetLength = alphabetLength;
		this.GEP = gep;

		this.alphabet = new Alphabet("TODO", alphabetLength);
	}

	/**
	 * Calculate the score between two characters (converted in integers)
	 * 
	 * @param a
	 * @param b
	 * @return
	 */
	public final float score(int a, int b) {
		// TODO - report code from C
		return 0f;
	}

}

Add sign of methods of SustitutionMatrix