Move genetics folder out of game folder, document subnamespaces of genetics namespace, move genetics::translation_table to genetics::codon::table

CMakeLists.txt

@@ -14,7 +14,6 @@ find_package(SDL2 REQUIRED COMPONENTS SDL2::SDL2-static SDL2::SDL2main CONFIG)
 find_package(OpenAL REQUIRED CONFIG)
 find_library(physfs REQUIRED NAMES physfs-static PATHS "${CMAKE_PREFIX_PATH}/lib")
 
-
 # Determine dependencies
 set(STATIC_LIBS
 	dr_wav

src/game/states/play-state.cpp

@@ -63,7 +63,7 @@
 #include "utility/gamma.hpp"
 
 #include "utility/bit-math.hpp"
-#include "game/genetics/genetics.hpp"
+#include "genetics/genetics.hpp"
 #include <iostream>
 #include <bitset>
 #include <ctime>

src/game/genetics/amino-acid.hpp → src/genetics/amino-acid.hpp

@@ -23,6 +23,8 @@
 #include <type_traits>
 
 namespace genetics {
+
+/// Functions which operate on IUPAC amino acid symbols.
 namespace amino_acid {
 
 /**

src/game/genetics/base.hpp → src/genetics/base.hpp

@@ -21,6 +21,8 @@
 #define ANTKEEPER_GENETICS_BASE_HPP
 
 namespace genetics {
+
+/// Functions which operate on IUPAC degenerate base symbols.
 namespace base {
 
 /**
@@ -40,6 +42,7 @@ int compare(char a, char b);
  */
 char transcribe(char symbol);
 
+/// Functions which operate on IUPAC degenerate **DNA** base symbols.
 namespace dna
 {
 	/**
@@ -51,6 +54,7 @@ namespace dna
 	char complement(char symbol);
 }
 
+/// Functions which operate on IUPAC degenerate **RNA** base symbols.
 namespace rna
 {
 	/**

src/game/genetics/codon.hpp → src/genetics/codon.hpp

@@ -21,8 +21,24 @@
 #define ANTKEEPER_GENETICS_CODON_HPP
 
 namespace genetics {
+
+/// Functions and structures related to triplets of IUPAC base symbols.
 namespace codon {
 
+/**
+ * Table for translating codons to amino acids.
+ *
+ * @see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
+ */
+struct table
+{
+	/// String of 64 IUPAC amino acid base symbols, in TCAG order.
+	const char* aas;
+	
+	/// String of 64 IUPAC amino acid base symbols, in TCAG order, where symbols other than `-` and `*` indicate a start codon and its amino acid.
+	const char* starts;
+};
+
 /**
  * Returns `true` if a codon is a start codon.
  *

src/game/genetics/genetics.hpp → src/genetics/genetics.hpp

@@ -29,6 +29,6 @@ namespace genetics {}
 #include "matrix.hpp"
 #include "protein.hpp"
 #include "sequence.hpp"
-#include "translation-table.hpp"
+#include "standard-code.hpp"
 
 #endif // ANTKEEPER_GENETICS_HPP

src/game/genetics/matrix.hpp → src/genetics/matrix.hpp

@@ -21,6 +21,8 @@
 #define ANTKEEPER_GENETICS_MATRIX_HPP
 
 namespace genetics {
+
+/// Substitution matrix constants.
 namespace matrix {
 
 /**

src/game/genetics/protein.hpp → src/genetics/protein.hpp

@@ -24,6 +24,8 @@
 #include <type_traits>
 
 namespace genetics {
+
+/// Functions which operate on sequences of IUPAC amino acid symbols.
 namespace protein {
 
 /**

src/game/genetics/sequence.hpp → src/genetics/sequence.hpp

@@ -22,12 +22,13 @@
 
 #include "base.hpp"
 #include "codon.hpp"
-#include "translation-table.hpp"
 #include <algorithm>
 #include <iterator>
 #include <random>
 
 namespace genetics {
+
+/// Functions and structures related to sequences of IUPAC degenerate base symbols.
 namespace sequence {
 
 /**
@@ -75,7 +76,7 @@ void crossover_n(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, Size co
  * @return First ORF in the sequence, or `{last, last}` if no ORF was found.
  */
 template <class ForwardIt>
-orf<ForwardIt> find_orf(ForwardIt first, ForwardIt last, const translation_table& table);
+orf<ForwardIt> find_orf(ForwardIt first, ForwardIt last, const codon::table& table);
 
 /**
  * Applies the given function to a randomly selected element in a range.
@@ -129,8 +130,9 @@ OutputIt transcribe(InputIt first, InputIt last, OutputIt d_first);
  * @return Output iterator to the element past the last element translated. 
  */
 template <class InputIt, class OutputIt>
-OutputIt translate(InputIt first, InputIt last, OutputIt d_first, const translation_table& table);
+OutputIt translate(InputIt first, InputIt last, OutputIt d_first, const codon::table& table);
 
+/// Functions which operate on sequences of IUPAC degenerate **DNA** base symbols.
 namespace dna
 {
 	/**
@@ -144,6 +146,7 @@ namespace dna
 	OutputIt complement(InputIt first, InputIt last, OutputIt d_first);
 }
 
+/// Functions which operate on sequences of IUPAC degenerate **RNA** base symbols.
 namespace rna
 {
 	/**
@@ -192,7 +195,7 @@ void crossover_n(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, Size co
 }
 
 template <class ForwardIt>
-orf<ForwardIt> find_orf(ForwardIt first, ForwardIt last, const translation_table& table)
+orf<ForwardIt> find_orf(ForwardIt first, ForwardIt last, const codon::table& table)
 {
 	ForwardIt second;
 	ForwardIt third;
@@ -307,7 +310,7 @@ inline OutputIt transcribe(InputIt first, InputIt last, OutputIt d_first)
 }
 
 template <class InputIt, class OutputIt>
-OutputIt translate(InputIt first, InputIt last, OutputIt d_first, const translation_table& table)
+OutputIt translate(InputIt first, InputIt last, OutputIt d_first, const codon::table& table)
 {
 	auto length = std::distance(first, last);
 	

src/game/genetics/translation-table.hpp → src/genetics/standard-code.hpp

@@ -17,27 +17,19 @@
  * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ANTKEEPER_GENETICS_TRANSLATION_TABLE_HPP
-#define ANTKEEPER_GENETICS_TRANSLATION_TABLE_HPP
+#ifndef ANTKEEPER_GENETICS_STANDARD_CODE_HPP
+#define ANTKEEPER_GENETICS_STANDARD_CODE_HPP
+
+#include "codon.hpp"
 
 namespace genetics {
 
 /**
- * Genetic code translation table.
+ * Codon table for standard genetic code.
  *
- * @see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
+ * @see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1
  */
-struct translation_table
-{
-	/// String of 64 IUPAC amino acid base symbols, in TCAG order.
-	const char* aas;
-	
-	/// String of 64 IUPAC amino acid base symbols, in TCAG order, where symbols other than `-` and `*` indicate a start codon and its amino acid.
-	const char* starts;
-};
-
-/// Translation table for standard genetic code.
-constexpr translation_table standard_code =
+constexpr codon::table standard_code =
 {
 	"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
 	"---M------**--*----M---------------M----------------------------",
@@ -45,4 +37,4 @@ constexpr translation_table standard_code =
 
 } // namespace genetics
 
-#endif // ANTKEEPER_GENETICS_TRANSLATION_TABLE_HPP
+#endif // ANTKEEPER_GENETICS_STANDARD_CODE_HPP