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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
/* Copied and adjusted from https://raw.githubusercontent.com/kloetzl/libdna/master/bench2/revcomp.cxx
* Credits go to Fabian Klötzl (@kloetzl - https://github.com/kloetzl)
*/
#include <benchmark/benchmark.h>
#include <random>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/views/char_to.hpp>
#include <seqan3/alphabet/views/complement.hpp>
#include <seqan3/test/performance/simd_dna4.hpp>
enum class tag
{
revcomp_dna4_inline,
seqan3_dna4,
seqan3_dna4_vector,
seqan3_dna4_simd,
seqan3_dna4_simd_vector
};
class allocator
{
public:
allocator() = delete;
allocator(allocator const &) = delete;
allocator & operator=(allocator const &) = delete;
allocator(allocator &&) = delete;
allocator & operator=(allocator &&) = delete;
~allocator()
{
std::free(forward);
std::free(reverse);
}
allocator(size_t const length)
{
forward = static_cast<char *>(std::malloc(length + 1));
reverse = static_cast<char *>(std::malloc(length + 1));
}
auto get() const
{
return std::make_tuple(forward, reverse);
}
private:
char * forward{nullptr};
char * reverse{nullptr};
};
static void generate_random_dna4_char_string(char * dest, size_t const length)
{
constexpr std::array<char, 8> dna4_chars{'A', 'C', 'G', 'T', 'a', 'c', 'g', 't'};
std::mt19937_64 random_engine{1729u};
std::uniform_int_distribution<size_t> random_index(0u, dna4_chars.size() - 1u);
auto random_dna4_char = [&dna4_chars, &random_engine, &random_index]()
{
return dna4_chars[random_index(random_engine)];
};
std::ranges::generate_n(dest, length, random_dna4_char);
dest[length - 1u] = '\0';
}
static constexpr char * revcomp_dna4_inline(char const * const begin, size_t const length, char * const dest)
{
for (size_t i = 0; i < length; ++i)
{
char c = begin[length - 1 - i];
dest[i] = c ^= c & 2 ? 4 : 21;
}
return dest + length;
}
static constexpr auto seqan3_dna4(std::string_view sv)
{
return sv | seqan3::views::char_to<seqan3::dna4> | std::views::reverse | seqan3::views::complement;
}
static void seqan3_dna4_vector(std::string_view sv, std::vector<seqan3::dna4> & dest)
{
auto revcomp = sv | seqan3::views::char_to<seqan3::dna4> | std::views::reverse | seqan3::views::complement;
std::ranges::copy(revcomp, dest.begin());
}
static constexpr auto seqan3_dna4_simd(std::string_view sv)
{
return sv | seqan3::views::char_to<seqan3::simd_dna4> | std::views::reverse | seqan3::views::complement;
}
static void seqan3_dna4_simd_vector(std::string_view sv, std::vector<seqan3::simd_dna4> & dest)
{
auto revcomp = sv | seqan3::views::char_to<seqan3::simd_dna4> | std::views::reverse | seqan3::views::complement;
std::ranges::copy(revcomp, dest.begin());
}
template <tag id>
void complement(benchmark::State & state)
{
constexpr size_t length{1'000'003};
allocator alloc{length};
auto [forward, revcomp] = alloc.get();
generate_random_dna4_char_string(forward, length);
auto sv = std::string_view{forward};
using alphabet_t = std::conditional_t<id == tag::seqan3_dna4_vector, seqan3::dna4, seqan3::simd_dna4>;
std::vector<alphabet_t> vector(length);
for (auto _ : state)
{
if constexpr (id == tag::revcomp_dna4_inline)
{
revcomp_dna4_inline(forward, length, revcomp);
benchmark::DoNotOptimize(revcomp);
}
else if constexpr (id == tag::seqan3_dna4)
{
auto view = seqan3_dna4(sv);
for (auto elem : view)
benchmark::DoNotOptimize(elem);
}
else if constexpr (id == tag::seqan3_dna4_vector)
{
seqan3_dna4_vector(sv, vector);
benchmark::DoNotOptimize(vector);
}
else if constexpr (id == tag::seqan3_dna4_simd)
{
auto view = seqan3_dna4_simd(sv);
for (auto elem : view)
benchmark::DoNotOptimize(elem);
}
else if constexpr (id == tag::seqan3_dna4_simd_vector)
{
seqan3_dna4_simd_vector(sv, vector);
benchmark::DoNotOptimize(vector);
}
else
{
throw std::logic_error{"Invalid tag"};
}
}
}
BENCHMARK_TEMPLATE(complement, tag::revcomp_dna4_inline);
BENCHMARK_TEMPLATE(complement, tag::seqan3_dna4);
BENCHMARK_TEMPLATE(complement, tag::seqan3_dna4_vector);
BENCHMARK_TEMPLATE(complement, tag::seqan3_dna4_simd);
BENCHMARK_TEMPLATE(complement, tag::seqan3_dna4_simd_vector);
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