/**
 * 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 {

}

@@ -669,16 +669,78 @@
 rithm;%0A%0A
+import com.salsaw.salsa.algorithm.exceptions.SALSAException;%0A%0A
 /**%0A * I
@@ -775,19 +775,16 @@
  matrix.
-%0A *
  The rol
@@ -810,16 +810,19 @@
 value of
+%0A *
  m(%CE%B1;%CE%B2) 
@@ -840,17 +840,16 @@
 d score.
- 
 %0A * %0A * 
@@ -851,16 +851,20 @@
  %0A * %3Cp%3E
+%0A * 
 Note: in
@@ -905,16 +905,20 @@
 an array
+%0A * 
 %3C/p%3E%0A * 
@@ -1029,10 +1029,773 @@
 trix %7B%0A%0A
+%09// FIELDS%0A%09private final int alphabetLength;%0A%09/**%0A%09 * GAP extension penalty%0A%09 */%0A%09private final float GEP;%0A%0A%09private final Alphabet alphabet;%0A%0A%09private final int%5B%5D matrix;%0A%0A%09// CONSTRUCTOR%0A%0A%09// GET/SET%0A%09public final Alphabet getAlphabet() %7B%0A%09%09return this.alphabet;%0A%09%7D%0A%0A%09public SubstitutionMatrix(String filePath, int alphabetLength, float gep)%0A%09%09%09throws SALSAException %7B%0A%09%09this.matrix = new int%5BalphabetLength * alphabetLength%5D;%0A%09%09this.alphabetLength = alphabetLength;%0A%09%09this.GEP = gep;%0A%0A%09%09this.alphabet = new Alphabet(%22TODO%22, alphabetLength);%0A%09%7D%0A%0A%09/**%0A%09 * Calculate the score between two characters (converted in integers)%0A%09 * %0A%09 * @param a%0A%09 * @param b%0A%09 * @return%0A%09 */%0A%09public final float score(int a, int b) %7B%0A%09%09// TODO - report code from C%0A%09%09return 0f;%0A%09%7D%0A%0A
 %7D%0A

Add sign of methods of SustitutionMatrix