Add dna translation function

src/game/genetics/translate.hpp

@@ -0,0 +1,94 @@
+/*
+ * Copyright (C) 2020  Christopher J. Howard
+ *
+ * This file is part of Antkeeper source code.
+ *
+ * Antkeeper source code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Antkeeper source code is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef ANTKEEPER_TRANSLATE_HPP
+#define ANTKEEPER_TRANSLATE_HPP
+
+#include <algorithm>
+#include <cstdint>
+#include <iterator>
+
+namespace dna
+{
+
+constexpr char* standard_code =
+	"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"  // Amino acid
+	"---M------**--*----M---------------M----------------------------"  // Start/stop
+	"TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG"  // Base 1
+	"TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG"  // Base 2
+	"TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"; // Base 3
+
+/**
+ * Translates codons into amino acids until a stop codon is read or the end of the sequence is reached.
+ *
+ * @param first,last Range of codons to translate.
+ * @param t_first Beginning of the translation table.
+ * @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)
+{
+	InputIt1 second = first;
+	++second;
+	InputIt1 third = second;
+	++third;
+	
+	InputIt2 base1_first = t_first;
+	std::advance(base1_first, 128);
+	InputIt2 base2_first = base1_first;
+	std::advance(base2_first, 64);
+	InputIt2 base3_first = base2_first;
+	std::advance(base3_first, 64);
+	
+	while (first != last && second != last && third != last)
+	{
+		InputIt2 aa = t_first;
+		InputIt2 base1 = base1_first;
+		InputIt2 base2 = base2_first;
+		InputIt2 base3 = base3_first;
+		
+		for (std::uint_fast8_t i = 0; i < 64; ++i)
+		{
+			if (*first == *base1 && *second == *base2 && *third == *base3)
+			{
+				if (*aa == '*')
+					return d_first;
+				
+				*(d_first++) = *aa;
+				break;
+			}
+			
+			++aa;
+			++base1;
+			++base2;
+			++base3;
+		}
+		
+		first = ++third;
+		second = ++third;
+		++third;
+	}
+	
+	return d_first;
+}
+
+} // namespace dna
+
+#endif // ANTKEEPER_TRANSLATE_HPP