Improve bitwise genetic functions

src/game/genetics/zygosity.hpp → src/game/genetics/allele.hpp

@@ -17,8 +17,8 @@
  * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ANTKEEPER_ZYGOSITY_HPP
-#define ANTKEEPER_ZYGOSITY_HPP
+#ifndef ANTKEEPER_ALLELE_HPP
+#define ANTKEEPER_ALLELE_HPP
 
 namespace dna
 {
@@ -55,4 +55,4 @@ inline constexpr bool heterozygous(T x) noexcept
 
 } // namespace dna
 
-#endif // ANTKEEPER_ZYGOSITY_HPP
+#endif // ANTKEEPER_ALLELE_HPP

src/game/genetics/bit-math.hpp

@@ -49,7 +49,7 @@ constexpr T bit_extract(T x, T mask) noexcept;
  * @param x Value to count.
  * @return Number of set bits in @p x.
  */
-template <typename T>
+template <class T>
 constexpr int popcount(T x) noexcept;
 
 /**
@@ -59,18 +59,18 @@ constexpr int popcount(T x) noexcept;
  * @param y Second value.
  * @return Hamming distance between @px and @p y.
  */	
-template <typename T>
+template <class T>
 constexpr int hamming_distance(T x, T y) noexcept;
 
 
-template <typename T>
+template <class T>
 constexpr T bit_merge(T a, T b, T mask) noexcept
 {
 	return a ^ ((a ^ b) & mask);
 }
 
 template <class T>
-constexpr T bit_pad(T x) noexcept
+constexpr T bit_expand(T x) noexcept
 {
 	x &= (1 << (sizeof(T) << 2)) - 1;
 	
@@ -81,25 +81,64 @@ constexpr T bit_pad(T x) noexcept
 	if constexpr(sizeof(T) >= 2)
 		x = (x ^ (x <<  4)) & T(0x0f0f0f0f0f0f0f0f);
 	
-	x = (x ^ (x <<  2)) & T(0x3333333333333333);
-	x = (x ^ (x <<  1)) & T(0x5555555555555555);
+	x = (x ^ (x << 2)) & T(0x3333333333333333);
+	x = (x ^ (x << 1)) & T(0x5555555555555555);
 	
 	return x;
 }
 
-template <typename T>
-constexpr T bit_interleave(T a, T b) noexcept
+template <class T, class U = T>
+constexpr U interleave(T a, T b) noexcept
 {
-	return (bit_pad(b) << 1) | bit_pad(a);
+	return bit_expand<U>(a) | (bit_expand<U>(b) << 1);
 }
 
-template <typename T>
+/**
+ * Returns the parity of a value.
+ *
+ * @param x Value to test.
+ * @return `1` if an odd number of bits are set, `0` otherwise.
+ */
+template <class T>
+constexpr T parity(T x) noexcept
+{
+	if constexpr(sizeof(T) >= 8)
+		x ^= x >> 32;
+	if constexpr(sizeof(T) >= 4)
+		x ^= x >> 16;
+	if constexpr(sizeof(T) >= 2)
+		x ^= x >> 8;
+	
+	x ^= x >> 4;
+	
+	return (0x6996 >> (x & 0xf)) & 1;
+}
+
+template <class T>
+constexpr T deinterleave(T x) noexcept
+{
+	x &= T(0x5555555555555555);
+	
+	x = (x ^ (x >> 1)) & T(0x3333333333333333);
+	x = (x ^ (x >> 2)) & T(0x0f0f0f0f0f0f0f0f);
+	
+	if constexpr(sizeof(T) >= 2)
+		x = (x ^ (x >>  4)) & T(0x00ff00ff00ff00ff);
+	if constexpr(sizeof(T) >= 4)
+		x = (x ^ (x >>  8)) & T(0x0000ffff0000ffff);
+	if constexpr(sizeof(T) >= 8)
+		x = (x ^ (x >> 16)) & T(0x00000000ffffffff);
+	
+	return x;
+}
+
+template <class T>
 constexpr T bit_swap_adjacent(T x) noexcept
 {
 	return ((x & T(0xaaaaaaaaaaaaaaaa)) >> 1) | ((x & T(0x5555555555555555)) << 1);
 }
 
-template <typename T>
+template <class T>
 constexpr T bit_shuffle_adjacent(T x, T mask) noexcept
 {
 	T y = bit_swap_adjacent(x);
@@ -169,7 +208,7 @@ constexpr T bit_extract(T x, T mask) noexcept
 	return result;
 }
 
-template <typename T>
+template <class T>
 constexpr int popcount(T x) noexcept
 {
 	int n = 0;
@@ -178,24 +217,12 @@ constexpr int popcount(T x) noexcept
 	return n;
 }
 
-template <typename T>
+template <class T>
 inline constexpr int hamming_distance(T x, T y) noexcept
 {
 	return popcount(x ^ y);
 }
 
-/**
- *
- * @param mask Least significant bits indicate whether to inherit the first (0) or second (1) allele from @p a. Most significant bits indicate whether to inherit the first (0) or second (1) allele from @p b.
- */
-template <class T>
-constexpr T inherit(T a, T b, T mask) noexcept
-{
-	a = bit_shuffle_adjacent<T>(a, mask);
-	b = bit_shuffle_adjacent<T>(b, mask >> (sizeof(T) << 2));
-	return bit_merge<T>(a, b, T(0x5555555555555555));
-}
-
 } // namespace dna
 
 #endif // ANTKEEPER_BIT_MATH_HPP

src/game/genetics/chromosome.hpp

@@ -0,0 +1,169 @@
+/*
+ * 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_CHROMOSOME_HPP
+#define ANTKEEPER_CHROMOSOME_HPP
+
+#include "bit-math.hpp"
+#include <array>
+
+namespace dna
+{
+
+/**
+ * Segregates the odd and even bits of a value.
+ *
+ * @param x Value to segregate.
+ * @return Value with even bits of @p x in the lower half, and odd bits in the upper half.
+ */
+template <class T>
+T segregate(T x)
+{
+	T odd = deinterleave(x);
+	T even = deinterleave(x >> 1);
+	
+	return odd | (even << (sizeof(T) << 2));
+}
+
+/**
+ * Interleaves bits of the lower and upper halves of a value.
+ *
+ * @param x Value to desegregate.
+ * @return Value with bits from the upper half of @p x interleaved with bits from the lower half.
+ */
+template <class T>
+T desegregate(T x)
+{
+	return interleave<T>(x, x >> (sizeof(T) << 2));
+}
+
+/**
+ * Replicates each bit in the lower half of a value.
+ *
+ * @param x Value to replicate.
+ * @return Value of @p x interleaved with itself.
+ */
+template <class T>
+T replicate(T x)
+{
+	x = bit_expand(x);
+	return x | (x << 1);
+}
+
+/**
+ * Performs 
+ */
+template <class T>
+std::array<T, 4> meiosis(T x, T mask)
+{
+	x = segregate(x);
+	T xl = x & (sizeof(T) << 2);
+	T xh = x >> (sizeof(T) << 2);
+	
+	T a = xl;
+	T b = crossover_n(xl, xh, mask);
+	T c = crossover_n(xh, xl, mask);
+	T d = xh;
+	
+	return {a, b, c, d};
+}
+
+/**
+ * 
+ *
+ * @param a 2c chromosome of first parent.
+ * @param b 2c chromosome of second parent.
+ * @param g Uniform random bit generator. `g()` will be called three times.
+ * @return 2c chromosome of child.
+ */
+template <class T, class URBG>
+T reproduce(T a, T b, URBG&& g)
+{
+	auto gametes_a = meiosis(a, static_cast<T>(g()));
+	auto gametes_b = meiosis(b, static_cast<T>(g()));
+	
+	T i = static_cast<T>(g());
+	T ca = gametes_a[i & 3];
+	T cb = gametes_b[(i >> 2) & 3];
+	
+	return interleave(ca, cb);
+}
+
+/**
+ * Performs a single-point crossover between two values.
+ *
+ * @param a First value.
+ * @param b Second value.
+ * @param i Index of the crossover point.
+ * @return Crossed over value.
+ */
+template <class T>
+constexpr T crossover(T a, T b, int i) noexcept;
+
+/**
+ * Performs an n-point crossover between two values.
+ *
+ * @param a First value.
+ * @param b Second value.
+ * @param mask Bit mask with set bits marking crossover points.
+ * @return Crossed over value.
+ */
+template <class T>
+constexpr T crossover_n(T a, T b, T mask) noexcept;
+
+/**
+ * Mutates a value by flipping a single bit.
+ *
+ * @param x Value to mutate.
+ * @param i Index of the bit to flip.
+ * @return Mutated copy of @p x.
+ */
+template <class T>
+T mutate(T x, int i);
+
+template <class T>
+inline constexpr T crossover(T a, T b, int i) noexcept
+{
+	T mask = (T(1) << i) - 1;
+	return bit_merge(b, a, mask);
+}
+
+template <class T>
+constexpr T crossover_n(T a, T b, T mask) noexcept
+{
+	T merge = ~T(0) * parity(mask);
+	
+	while (mask)
+	{
+		merge ^= (mask ^ (mask - 1)) >> 1;
+		mask &= mask - 1;
+	}
+	
+	return bit_merge(a, b, merge);
+}
+
+template <class T>
+inline T mutate(T x, int i)
+{
+	return x ^ (T(1) << i);
+}
+
+} // namespace dna
+
+#endif // ANTKEEPER_CHROMOSOME_HPP

src/game/genetics/crossover.hpp

@@ -1,74 +0,0 @@
-/*
- * 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_CROSSOVER_HPP
-#define ANTKEEPER_CROSSOVER_HPP
-
-#include "bit-math.hpp"
-
-namespace dna
-{
-
-/**
- * Performs a single-point crossover between two values.
- *
- * @param a First value.
- * @param b Second value.
- * @parma pos Position of the crossover point.
- */
-template <class T>
-constexpr T crossover(T a, T b, int pos) noexcept;
-
-/**
- * Performs an n-point crossover between two values.
- *
- * @param a First value.
- * @param b Second value.
- * @param mask Bit mask with set bits marking crossover points.
- */
-template <class T>
-constexpr T crossover_n(T a, T b, T mask) noexcept;
-
-template <class T>
-inline constexpr T crossover(T a, T b, int pos) noexcept
-{
-	T mask = (T(1) << pos) - 1;
-	return bit_merge(b, a, mask);
-}
-
-template <class T>
-constexpr T crossover_n(T a, T b, T mask) noexcept
-{
-	T merge = 0, i = 0;
-	
-	while (mask)
-	{
-		merge ^= (mask ^ (mask - 1)) >> 1;
-		mask &= mask - 1;
-		i = !i;
-	}
-	
-	merge ^= ~T(0) * i;
-	
-	return bit_merge<T>(a, b, merge);
-}
-
-} // namespace dna
-
-#endif // ANTKEEPER_CROSSOVER_HPP

src/game/genetics/gene.hpp

@@ -0,0 +1,56 @@
+/*
+ * 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_GENE_HPP
+#define ANTKEEPER_GENE_HPP
+
+namespace dna
+{
+
+/**
+ * Isolates a pair of bits and returns them in the two least significant bits.
+ *
+ * @param x Diploid chromosome with interleaved alleles.
+ * @param i Index of the pair to isolate.
+ * @return Isolated pair of bits in the two least significant bits.
+ */
+template <class T>
+T isolate(T x, int i)
+{
+	return (x >> (i << 1)) & 0b11;
+}
+
+/**
+ * Isolates a sequence of genes and returns their alleles in the least significant bits.
+ *
+ * @param x Diploid chromosome with interleaed alleles.
+ * @param i Index of the first gene in the sequence.
+ * @param n Length of the sequence, in genes.
+ * @return Alleles of the sequeuence in the least significant bits.
+ */
+template <class T>
+T isolate_n(T x, int i, int n)
+{
+	T mask = (T(1) << (n << 1)) - 1;
+	return (x >> (i << 1)) & mask;
+}
+
+} // namespace dna
+
+#endif // ANTKEEPER_GENE_HPP

src/game/genetics/mutate.hpp → src/game/genetics/trait.hpp

@@ -17,25 +17,24 @@
  * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ANTKEEPER_MUTATE_HPP
-#define ANTKEEPER_MUTATE_HPP
+#ifndef ANTKEEPER_TRAIT_HPP
+#define ANTKEEPER_TRAIT_HPP
 
 namespace dna
 {
 
-/**
- * Mutates a value by flipping a single bit.
- *
- * @param x Value to mutate.
- * @param i Index of the bit to flip.
- * @return Mutated copy of @p x.
- */
-template <class T>
-T mutate(T x, int i)
+template <typename T>
+T mendelian_variant(T x)
+{
+	return !!x;
+}
+
+template <typename T>
+T nonmendelian_variant(T x)
 {
-	return x ^ (T(1) << i);
+	return popcount(x);
 }
 
 } // namespace dna
 
-#endif // ANTKEEPER_MUTATE_HPP
+#endif // ANTKEEPER_TRAIT_HPP