From af8b516e7a49523d765900b0cb362fb78ee3ee0f Mon Sep 17 00:00:00 2001
From: "C. J. Howard" <cjhoward@protonmail.com>
Date: Sat, 26 Dec 2020 20:39:11 +0800
Subject: [PATCH] Document genetics::protein::identity function

---
 src/game/genetics/protein.hpp | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/src/game/genetics/protein.hpp b/src/game/genetics/protein.hpp
index 4e3ab38..3786f2b 100644
--- a/src/game/genetics/protein.hpp
+++ b/src/game/genetics/protein.hpp
@@ -26,11 +26,21 @@
 namespace genetics {
 namespace protein {
 
+/**
+ * Returns the percent identity 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 identity between the two proteins.
+ */
+template <class T, class ForwardIt1, class ForwardIt2>
+T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2);
+
 /**
  * Scores two proteins using a substitution matrix.
  *
- * @param first1,last1 Sequence of IUPAC amino acid codes which constitute the first protein.
- * @param first2,last2 Sequence of IUPAC amino acid codes which constitute the second protein.
+ * @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 matrix Substitution matrix.
  * @return Score of the two proteins.
  */
@@ -46,6 +56,19 @@ typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardI
 	return result;
 }
 
+template <class T, class ForwardIt1, class ForwardIt2>
+T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2)
+{
+	auto length = std::distance(first1, last1);
+	
+	T sum = 0;
+	for (; first1 != last1; ++first1, ++first2)
+		if (*first1 == *first2)
+			++sum;
+	
+	return sum / static_cast<T>(length);
+}
+
 } // namespace protein
 } // namespace genetics