From b6947b38425c46945e3e149623243755c8df855d Mon Sep 17 00:00:00 2001
From: "C. J. Howard" <cjhoward@protonmail.com>
Date: Sat, 19 Dec 2020 22:37:58 +0800
Subject: [PATCH] Add functions for finding start and stop codons

---
 src/game/genetics/translate.hpp | 113 +++++++++++++++++++++++++++++++-
 1 file changed, 112 insertions(+), 1 deletion(-)

diff --git a/src/game/genetics/translate.hpp b/src/game/genetics/translate.hpp
index 44987a9..327fa52 100644
--- a/src/game/genetics/translate.hpp
+++ b/src/game/genetics/translate.hpp
@@ -27,6 +27,7 @@
 namespace dna
 {
 
+/// Standard genetic code translation table.
 constexpr char* standard_code =
 	"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"  // Amino acid
 	"---M------**--*----M---------------M----------------------------"  // Start/stop
@@ -42,6 +43,116 @@ constexpr char* standard_code =
  * @param d_first Beginning of the destination range.
  * @return Output iterator to the amino acid in the destination range, one past the last amino acid translated.
  */
+template <class InputIt1, class InputIt2, class OutputIt>
+OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_first);
+
+/**
+ * Finds the first start codon in a sequence of bases.
+ *
+ * @param first,last Range of bases to search.
+ * @param t_first Beginning of the translation table.
+ * @return Iterator to the first base of the first start codon in the sequence, or @p last if no start codon is found.
+ */
+template <class ForwardIt1, class ForwardIt2>
+ForwardIt1 find_start(ForwardIt1 first, ForwardIt1 last, ForwardIt2 t_first);
+
+/**
+ * Finds the first stop codon in a sequence of codons.
+ *
+ * @param first,last Range of codons to search.
+ * @param t_first Beginning of the translation table.
+ * @return Iterator to the first base of the first stop codon in the sequence, or @p last if no stop codon is found.
+ */
+template <class ForwardIt1, class ForwardIt2>
+ForwardIt1 find_stop(ForwardIt1 first, ForwardIt1 last, ForwardIt2 t_first);
+
+template <class ForwardIt1, class ForwardIt2>
+ForwardIt1 find_start(ForwardIt1 first, ForwardIt1 last, ForwardIt2 t_first)
+{
+	ForwardIt1 second = first;
+	++second;
+	ForwardIt1 third = second;
+	++third;
+	
+	ForwardIt2 start_first = t_first;
+	std::advance(start_first, 64);
+	ForwardIt2 base1_first = start_first;
+	std::advance(base1_first, 64);
+	ForwardIt2 base2_first = base1_first;
+	std::advance(base2_first, 64);
+	ForwardIt2 base3_first = base2_first;
+	std::advance(base3_first, 64);
+	
+	if (first != last && second != last)
+	{
+		while (third != last)
+		{
+			ForwardIt2 start = start_first;
+			ForwardIt2 base1 = base1_first;
+			ForwardIt2 base2 = base2_first;
+			ForwardIt2 base3 = base3_first;
+			
+			for (std::uint_fast8_t i = 64; i; --i)
+			{
+				if (*start != '-' && *start != '*' && *first == *base1 && *second == *base2 && *third == *base3)
+					return first;
+				
+				++start;
+				++base1;
+				++base2;
+				++base3;
+			}
+			
+			first = second;
+			second = third;
+			++third;
+		}
+	}
+	
+	return last;
+}
+
+template <class ForwardIt1, class ForwardIt2>
+ForwardIt1 find_stop(ForwardIt1 first, ForwardIt1 last, ForwardIt2 t_first)
+{
+	ForwardIt1 second = first;
+	++second;
+	ForwardIt1 third = second;
+	++third;
+	
+	ForwardIt2 base1_first = t_first;
+	std::advance(base1_first, 128);
+	ForwardIt2 base2_first = base1_first;
+	std::advance(base2_first, 64);
+	ForwardIt2 base3_first = base2_first;
+	std::advance(base3_first, 64);
+	
+	while (first != last && second != last && third != last)
+	{
+		ForwardIt2 aa = t_first;
+		ForwardIt2 base1 = base1_first;
+		ForwardIt2 base2 = base2_first;
+		ForwardIt2 base3 = base3_first;
+		
+		for (std::uint_fast8_t i = 64; i; --i)
+		{
+			if (*aa == '*' && *first == *base1 && *second == *base2 && *third == *base3)
+				return first;
+			
+			++aa;
+			++base1;
+			++base2;
+			++base3;
+		}
+		
+		first = ++third;
+		second = ++third;
+		++third;
+	}
+	
+	return last;
+}
+
 template <class InputIt1, class InputIt2, class OutputIt>
 OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_first)
 {
@@ -64,7 +175,7 @@ OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_f
 		InputIt2 base2 = base2_first;
 		InputIt2 base3 = base3_first;
 		
-		for (std::uint_fast8_t i = 0; i < 64; ++i)
+		for (std::uint_fast8_t i = 64; i; --i)
 		{
 			if (*first == *base1 && *second == *base2 && *third == *base3)
 			{