From eea8665dcd3924464add4c1f63bfa0329fd4b6dc Mon Sep 17 00:00:00 2001
From: "C. J. Howard" <cjhoward@protonmail.com>
Date: Sat, 19 Dec 2020 23:03:31 +0800
Subject: [PATCH] Add DNA transcription functions

---
 src/game/genetics/crossover.hpp               |  6 ++--
 src/game/genetics/mutate.hpp                  |  6 ++--
 .../genetics/{trait.hpp => transcribe.hpp}    | 36 ++++++++++++++-----
 src/game/genetics/translate.hpp               |  8 ++---
 4 files changed, 37 insertions(+), 19 deletions(-)
 rename src/game/genetics/{trait.hpp => transcribe.hpp} (50%)

diff --git a/src/game/genetics/crossover.hpp b/src/game/genetics/crossover.hpp
index 4cae2ed..7bb3eaf 100644
--- a/src/game/genetics/crossover.hpp
+++ b/src/game/genetics/crossover.hpp
@@ -17,8 +17,8 @@
  * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ANTKEEPER_CROSSOVER_HPP
-#define ANTKEEPER_CROSSOVER_HPP
+#ifndef ANTKEEPER_DNA_CROSSOVER_HPP
+#define ANTKEEPER_DNA_CROSSOVER_HPP
 
 #include <algorithm>
 #include <iterator>
@@ -85,4 +85,4 @@ void crossover_n(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, Size co
 
 } // namespace dna
 
-#endif // ANTKEEPER_CROSSOVER_HPP
+#endif // ANTKEEPER_DNA_CROSSOVER_HPP
diff --git a/src/game/genetics/mutate.hpp b/src/game/genetics/mutate.hpp
index d4dc2d2..fee49eb 100644
--- a/src/game/genetics/mutate.hpp
+++ b/src/game/genetics/mutate.hpp
@@ -17,8 +17,8 @@
  * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ANTKEEPER_MUTATE_HPP
-#define ANTKEEPER_MUTATE_HPP
+#ifndef ANTKEEPER_DNA_MUTATE_HPP
+#define ANTKEEPER_DNA_MUTATE_HPP
 
 #include <algorithm>
 #include <iterator>
@@ -80,4 +80,4 @@ void mutate_n(ForwardIt first, ForwardIt last, Size count, UnaryOperation unary_
 
 } // namespace dna
 
-#endif // ANTKEEPER_MUTATE_HPP
+#endif // ANTKEEPER_DNA_MUTATE_HPP
diff --git a/src/game/genetics/trait.hpp b/src/game/genetics/transcribe.hpp
similarity index 50%
rename from src/game/genetics/trait.hpp
rename to src/game/genetics/transcribe.hpp
index 5d019ff..237c3fc 100644
--- a/src/game/genetics/trait.hpp
+++ b/src/game/genetics/transcribe.hpp
@@ -17,24 +17,42 @@
  * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ANTKEEPER_TRAIT_HPP
-#define ANTKEEPER_TRAIT_HPP
+#ifndef ANTKEEPER_DNA_TRANSCRIBE_HPP
+#define ANTKEEPER_DNA_TRANSCRIBE_HPP
+
+#include <algorithm>
 
 namespace dna
 {
 
-template <typename T>
-T mendelian_variant(T x)
+/**
+ * Transcribes DNA into RNA, replacing all occurences of `T` with `U`.
+ *
+ * @param first,last Range of DNA bases to transcribe.
+ */
+template <class ForwardIt>
+void transcribe(ForwardIt first, ForwardIt last);
+
+/**
+ * Transcribes RNA back into DNA, replacing all occurences of `U` with `T`.
+ *
+ * @param first,last Range of RNA bases to transcribe.
+ */
+template <class ForwardIt>
+void untranscribe(ForwardIt first, ForwardIt last);
+
+template <class ForwardIt>
+void transcribe(ForwardIt first, ForwardIt last)
 {
-	return !!x;
+	std::replace(first, last, 'T', 'U');
 }
 
-template <typename T>
-T nonmendelian_variant(T x)
+template <class ForwardIt>
+void untranscribe(ForwardIt first, ForwardIt last)
 {
-	return popcount(x);
+	std::replace(first, last, 'U', 'T');
 }
 
 } // namespace dna
 
-#endif // ANTKEEPER_TRAIT_HPP
+#endif // ANTKEEPER_DNA_TRANSCRIBE_HPP
diff --git a/src/game/genetics/translate.hpp b/src/game/genetics/translate.hpp
index 327fa52..c071cc9 100644
--- a/src/game/genetics/translate.hpp
+++ b/src/game/genetics/translate.hpp
@@ -17,8 +17,8 @@
  * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ANTKEEPER_TRANSLATE_HPP
-#define ANTKEEPER_TRANSLATE_HPP
+#ifndef ANTKEEPER_DNA_TRANSLATE_HPP
+#define ANTKEEPER_DNA_TRANSLATE_HPP
 
 #include <algorithm>
 #include <cstdint>
@@ -27,7 +27,7 @@
 namespace dna
 {
 
-/// Standard genetic code translation table.
+/// DNA translation table for standard genetic code.
 constexpr char* standard_code =
 	"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"  // Amino acid
 	"---M------**--*----M---------------M----------------------------"  // Start/stop
@@ -202,4 +202,4 @@ OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_f
 
 } // namespace dna
 
-#endif // ANTKEEPER_TRANSLATE_HPP
+#endif // ANTKEEPER_DNA_TRANSLATE_HPP