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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
#include <benchmark/benchmark.h>
#include <deque>
#include <list>
#include <vector>
#include <seqan3/alignment/decorator/gap_decorator.hpp>
#include <seqan3/alphabet/all.hpp>
#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
#include <seqan3/contrib/sdsl-lite.hpp>
#include <seqan3/test/performance/sequence_generator.hpp>
#include <seqan3/test/seqan2.hpp>
#include <seqan3/utility/container/small_vector.hpp>
template <typename t>
using sdsl_int_vec = seqan3::contrib::sdsl::int_vector<sizeof(t) * 8>;
template <typename t>
using small_vec = seqan3::small_vector<t, 10000>;
// ============================================================================
// sequential_read
// ============================================================================
template <template <typename...> typename container_t,
typename alphabet_t,
bool const_qualified = false,
typename... args>
void sequential_read(benchmark::State & state)
{
container_t<alphabet_t, args...> container = []()
{
auto container = seqan3::test::generate_sequence<alphabet_t>(10000, 0, 0);
return container_t<alphabet_t, args...>(container.begin(), container.end());
}();
using container_reference_t = std::
conditional_t<const_qualified, container_t<alphabet_t, args...> const &, container_t<alphabet_t, args...> &>;
container_reference_t container_reference{container};
alphabet_t letter{};
for (auto _ : state)
for (auto && element : container_reference)
benchmark::DoNotOptimize(letter = element);
state.counters["sizeof"] = sizeof(alphabet_t);
if constexpr (seqan3::alphabet<alphabet_t>)
state.counters["alph_size"] = seqan3::alphabet_size<alphabet_t>;
state.counters["const"] = const_qualified;
}
BENCHMARK_TEMPLATE(sequential_read, std::vector, char);
BENCHMARK_TEMPLATE(sequential_read, std::vector, uint8_t);
BENCHMARK_TEMPLATE(sequential_read, std::vector, uint16_t);
BENCHMARK_TEMPLATE(sequential_read, std::vector, uint32_t);
BENCHMARK_TEMPLATE(sequential_read, std::vector, uint64_t);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::gap);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::dna4);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::dna5);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::gapped<seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::dna15);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::aa27);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::qualified<seqan3::dna4, seqan3::phred42>);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::alphabet_variant<char, seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, std::deque, char);
BENCHMARK_TEMPLATE(sequential_read, std::deque, uint8_t);
BENCHMARK_TEMPLATE(sequential_read, std::deque, uint16_t);
BENCHMARK_TEMPLATE(sequential_read, std::deque, uint32_t);
BENCHMARK_TEMPLATE(sequential_read, std::deque, uint64_t);
BENCHMARK_TEMPLATE(sequential_read, std::deque, seqan3::gap);
BENCHMARK_TEMPLATE(sequential_read, std::deque, seqan3::dna4);
BENCHMARK_TEMPLATE(sequential_read, std::deque, seqan3::dna5);
BENCHMARK_TEMPLATE(sequential_read, std::deque, seqan3::gapped<seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, std::deque, seqan3::dna15);
BENCHMARK_TEMPLATE(sequential_read, std::deque, seqan3::aa27);
BENCHMARK_TEMPLATE(sequential_read, std::deque, seqan3::qualified<seqan3::dna4, seqan3::phred42>);
BENCHMARK_TEMPLATE(sequential_read, std::deque, seqan3::alphabet_variant<char, seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, std::list, char);
BENCHMARK_TEMPLATE(sequential_read, std::list, uint8_t);
BENCHMARK_TEMPLATE(sequential_read, std::list, uint16_t);
BENCHMARK_TEMPLATE(sequential_read, std::list, uint32_t);
BENCHMARK_TEMPLATE(sequential_read, std::list, uint64_t);
BENCHMARK_TEMPLATE(sequential_read, std::list, seqan3::gap);
BENCHMARK_TEMPLATE(sequential_read, std::list, seqan3::dna4);
BENCHMARK_TEMPLATE(sequential_read, std::list, seqan3::dna5);
BENCHMARK_TEMPLATE(sequential_read, std::list, seqan3::gapped<seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, std::list, seqan3::dna15);
BENCHMARK_TEMPLATE(sequential_read, std::list, seqan3::aa27);
BENCHMARK_TEMPLATE(sequential_read, std::list, seqan3::qualified<seqan3::dna4, seqan3::phred42>);
BENCHMARK_TEMPLATE(sequential_read, std::list, seqan3::alphabet_variant<char, seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, sdsl_int_vec, uint8_t);
BENCHMARK_TEMPLATE(sequential_read, sdsl_int_vec, uint16_t);
BENCHMARK_TEMPLATE(sequential_read, sdsl_int_vec, uint32_t);
BENCHMARK_TEMPLATE(sequential_read, sdsl_int_vec, uint64_t);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, char);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, uint32_t);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::gap);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::dna4);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::dna5);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::gapped<seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::dna15);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::aa27);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::qualified<seqan3::dna4, seqan3::phred42>);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::alphabet_variant<char, seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, small_vec, char);
BENCHMARK_TEMPLATE(sequential_read, small_vec, uint32_t);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::gap);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::dna4);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::dna5);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::gapped<seqan3::dna4>);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::dna15);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::aa27);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::qualified<seqan3::dna4, seqan3::phred42>);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::alphabet_variant<char, seqan3::dna4>);
// ============================================================================
// sequential_read (const)
// ============================================================================
BENCHMARK_TEMPLATE(sequential_read, std::vector, char, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, uint8_t, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, uint16_t, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, uint32_t, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, uint64_t, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::gap, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::dna4, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::dna5, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::gapped<seqan3::dna4>, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::dna15, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::aa27, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::qualified<seqan3::dna4, seqan3::phred42>, true);
BENCHMARK_TEMPLATE(sequential_read, std::vector, seqan3::alphabet_variant<char, seqan3::dna4>, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, char, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, uint32_t, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::gap, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::dna4, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::dna5, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::gapped<seqan3::dna4>, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::dna15, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::aa27, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::qualified<seqan3::dna4, seqan3::phred42>, true);
BENCHMARK_TEMPLATE(sequential_read, seqan3::bitpacked_sequence, seqan3::alphabet_variant<char, seqan3::dna4>, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, char, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, uint32_t, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::gap, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::dna4, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::dna5, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::gapped<seqan3::dna4>, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::dna15, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::aa27, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::qualified<seqan3::dna4, seqan3::phred42>, true);
BENCHMARK_TEMPLATE(sequential_read, small_vec, seqan3::alphabet_variant<char, seqan3::dna4>, true);
// ============================================================================
// SeqAn2: sequential_read
// ============================================================================
#if SEQAN3_HAS_SEQAN2
# include <seqan/sequence.h>
template <template <typename...> typename container_t,
typename spec_t,
typename alphabet_t,
bool const_qualified = false>
void sequential_read2(benchmark::State & state)
{
container_t<alphabet_t, spec_t> container{seqan3::test::generate_sequence_seqan2<alphabet_t>(10000, 0, 0)};
using container_reference_t =
std::conditional_t<const_qualified, container_t<alphabet_t, spec_t> const &, container_t<alphabet_t, spec_t> &>;
container_reference_t container_reference{container};
alphabet_t letter{};
for (auto _ : state)
for (auto && element : container_reference)
benchmark::DoNotOptimize(letter = element);
state.counters["sizeof"] = sizeof(alphabet_t);
state.counters["alph_size"] = seqan2::ValueSize<alphabet_t>::VALUE;
state.counters["const"] = const_qualified;
}
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, char);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, uint8_t);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, uint16_t);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, uint32_t);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, uint64_t);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::Dna);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::Dna5);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::Iupac);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::AminoAcid);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::Dna5Q);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Dna);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Dna5);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Iupac);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::AminoAcid);
// BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Dna5Q); // broken in SeqAn2
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::Dna);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::Dna5);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::Iupac);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::AminoAcid);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::Dna5Q);
// ============================================================================
// sequential_read (const)
// ============================================================================
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, char, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, uint8_t, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, uint16_t, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, uint32_t, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, uint64_t, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::Dna, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::Dna5, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::Iupac, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::AminoAcid, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Alloc<>, seqan2::Dna5Q, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Dna, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Dna5, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Iupac, true);
BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::AminoAcid, true);
// BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Dna5Q); // broken in SeqAn2
#endif // SEQAN3_HAS_SEQAN2
// ============================================================================
// run
// ============================================================================
BENCHMARK_MAIN();
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