Add function for calculating the percent similarity between two proteins

src/game/genetics/protein.hpp

@@ -40,21 +40,22 @@ T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2);
  * Scores two proteins using a substitution matrix.
  *
  * @param first1,last1 Range of IUPAC amino acid codes which constitute the first protein.
- * @param first2,last2 Range of IUPAC amino acid codes which constitute the second protein.
+ * @param first2 Beginning of the range of IUPAC amino acid codes which constitute the second protein.
  * @param matrix Substitution matrix.
  * @return Score of the two proteins.
  */
 template <class ForwardIt1, class ForwardIt2, class Matrix>
-typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, ForwardIt2 last2, const Matrix& matrix);
+typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix);
 
-template <class ForwardIt1, class ForwardIt2, class Matrix>
-typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, ForwardIt2 last2, const Matrix& matrix)
-{
-	typename std::remove_all_extents<Matrix>::type result = 0;
-	for (; first1 != last1 && first2 != last2; ++first1, ++first2)
-		result += amino_acid::score(*first1, *first2, matrix);
-	return result;
-}
+/**
+ * Returns the percent similarity between two proteins.
+ *
+ * @param first1,last1 Range of IUPAC amino acids which constitute the first protein.
+ * @param first2 Beginning of the range of IUPAC amino acids which constitute the second protein.
+ * @return Percent similarity between the two proteins.
+ */
+template <class T, class ForwardIt1, class ForwardIt2, class Matrix>
+typename T similarity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix);
 
 template <class T, class ForwardIt1, class ForwardIt2>
 T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2)
@@ -69,6 +70,28 @@ T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2)
 	return sum / static_cast<T>(length);
 }
 
+template <class ForwardIt1, class ForwardIt2, class Matrix>
+typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix)
+{
+	typename std::remove_all_extents<Matrix>::type result = 0;
+	for (; first1 != last1; ++first1, ++first2)
+		result += amino_acid::score(*first1, *first2, matrix);
+	return result;
+}
+
+template <class T, class ForwardIt1, class ForwardIt2, class Matrix>
+typename T similarity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix)
+{
+	T length = static_cast<T>(std::distance(first1, last1));
+	T positive_count = T(0);
+	
+	for (; first1 != last1; ++first1, ++first2)
+		if (amino_acid::score(*first1, *first2, matrix) > 0)
+			++positive_count;
+	
+	return positive_count / length;
+}
+
 } // namespace protein
 } // namespace genetics