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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 <sstream>
#include <string>
#include <seqan3/alphabet/nucleotide/rna4.hpp>
#include <seqan3/alphabet/views/to_char.hpp>
#include <seqan3/io/structure_file/format_vienna.hpp>
#include <seqan3/io/structure_file/input.hpp>
#include <seqan3/io/structure_file/output.hpp>
#include <seqan3/test/performance/sequence_generator.hpp>
#include <seqan3/test/performance/units.hpp>
#include <seqan3/test/seqan2.hpp>
#include <seqan3/utility/range/to.hpp>
#if SEQAN3_HAS_SEQAN2
# include <seqan/rna_io.h>
#endif
inline constexpr size_t iterations_per_run = 1024;
static std::string const header{"seq foobar blobber"};
static inline auto const rna_sequence = seqan3::test::generate_sequence<seqan3::rna4>(474, 0, 0);
static auto const sequence = rna_sequence | seqan3::views::to_char | seqan3::ranges::to<std::string>();
static std::string const structure{"(((((((..((((........)))).((((.........)))).....(((((.......))))))))))))......."
"(((((((..((((........)))).((((.........)))).....(((((.......))))))))))))......."
"(((((((..((((........)))).((((.........)))).....(((((.......))))))))))))......."
"(((((((..((((........)))).((((.........)))).....(((((.......))))))))))))......."
"(((((((..((((........)))).((((.........)))).....(((((.......))))))))))))......."
"(((((((..((((........)))).((((.........)))).....(((((.......))))))))))))......."};
static std::string const vienna_file = []()
{
std::string file{};
for (size_t idx = 0; idx < iterations_per_run; idx++)
file += "> " + header + "\n" + sequence + "\n" + structure + "\n";
return file;
}();
void write_seqan3(benchmark::State & state)
{
std::ostringstream ostream;
seqan3::structure_file_output fout{ostream, seqan3::format_vienna{}};
for (auto _ : state)
{
for (size_t idx = 0; idx < iterations_per_run; ++idx)
fout.emplace_back(sequence, header, structure);
}
ostream = std::ostringstream{};
fout.emplace_back(sequence, header, structure);
size_t bytes_per_run = ostream.str().size() * iterations_per_run;
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(write_seqan3);
#if SEQAN3_HAS_SEQAN2
void write_seqan2(benchmark::State & state)
{
std::ostringstream ostream;
seqan2::RnaRecord record{};
record.name = header;
record.sequence = sequence;
seqan2::bracket2graph(record.fixedGraphs, structure);
for (auto _ : state)
{
for (size_t idx = 0; idx < iterations_per_run; ++idx)
seqan2::writeRecord(ostream, record, seqan2::Vienna());
}
ostream = std::ostringstream{};
seqan2::writeRecord(ostream, record, seqan2::Vienna());
size_t bytes_per_run = ostream.str().size() * iterations_per_run;
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(write_seqan2);
#endif
void read_seqan3(benchmark::State & state)
{
std::istringstream istream{vienna_file};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}};
for (auto _ : state)
{
istream.clear();
istream.seekg(0, std::ios::beg);
auto it = fin.begin();
for (size_t idx = 0; idx < iterations_per_run; ++idx)
it++;
}
size_t bytes_per_run = vienna_file.size();
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(read_seqan3);
#if SEQAN3_HAS_SEQAN2
void read_seqan2(benchmark::State & state)
{
seqan2::RnaRecord record{};
std::istringstream istream{vienna_file};
for (auto _ : state)
{
istream.clear();
istream.seekg(0, std::ios::beg);
auto it = seqan2::Iter<std::istringstream, seqan2::StreamIterator<seqan2::Input>>(istream);
for (size_t idx = 0; idx < iterations_per_run; ++idx)
{
seqan2::readRecord(record, it, seqan2::Vienna());
clear(record);
}
}
size_t bytes_per_run = vienna_file.size();
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(read_seqan2);
#endif
BENCHMARK_MAIN();
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