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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#include <random>
#include <vector>
#include <benchmark/benchmark.h>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/range/views/join.hpp>
#include <seqan3/range/views/to.hpp>
#include <seqan3/range/views/translate.hpp>
#include <seqan3/range/views/translate_join.hpp>
#include <seqan3/test/performance/sequence_generator.hpp>
#include <seqan3/test/seqan2.hpp>
#ifdef SEQAN3_HAS_SEQAN2
#include <seqan/sequence.h>
#include <seqan/seq_io.h>
#include <seqan/translation.h>
#endif
// Tags used to define the benchmark type
struct baseline_tag{}; // Baseline where view is applied and only iterating the output range is benchmarked
struct translate_tag{}; // Benchmark view_translate followed by seqan3::views::join
struct translate_join_tag{}; // Benchmark seqan3::views::translate_join
// ============================================================================
// sequential_read
// ============================================================================
template <typename rng_t>
void sequential_read_impl(benchmark::State & state, rng_t && rng)
{
for (auto _ : state)
for (auto && outer : rng)
benchmark::DoNotOptimize(outer[0].to_rank());
}
template <typename tag_t>
void sequential_read(benchmark::State & state)
{
std::vector<std::vector<seqan3::dna4>> dna_sequence_collection{};
dna_sequence_collection.resize(1000);
for (size_t i = 0; i < dna_sequence_collection.size(); ++i)
dna_sequence_collection[i] = seqan3::test::generate_sequence<seqan3::dna4>(100, 0, 0);
if constexpr (std::is_same_v<tag_t, baseline_tag>)
{
std::vector<seqan3::aa27_vector> translated_aa_sequences = dna_sequence_collection
| seqan3::views::translate_join
| seqan3::views::to<std::vector<seqan3::aa27_vector>>;
sequential_read_impl(state, translated_aa_sequences);
}
else if constexpr (std::is_same_v<tag_t, translate_tag>)
{
auto translated_aa_view = dna_sequence_collection | seqan3::views::translate | seqan3::views::join;
sequential_read_impl(state, translated_aa_view);
}
else
{
auto translated_aa_view = dna_sequence_collection | seqan3::views::translate_join;
sequential_read_impl(state, translated_aa_view);
}
}
BENCHMARK_TEMPLATE(sequential_read, baseline_tag);
BENCHMARK_TEMPLATE(sequential_read, translate_tag);
BENCHMARK_TEMPLATE(sequential_read, translate_join_tag);
// ============================================================================
// random_access
// ============================================================================
template <typename rng_t>
void random_access_impl(benchmark::State & state, rng_t && rng, std::vector<size_t> const & access_positions)
{
for (auto _ : state)
for (auto pos : access_positions)
benchmark::DoNotOptimize(rng[pos][0].to_rank());
}
template <typename tag_t>
void random_access(benchmark::State & state)
{
std::vector<std::vector<seqan3::dna4>> dna_sequence_collection{};
dna_sequence_collection.resize(1000);
for (size_t i = 0; i < dna_sequence_collection.size(); ++i)
dna_sequence_collection[i] = seqan3::test::generate_sequence<seqan3::dna4>(100, 0, 0);
std::vector<size_t> access_positions{};
access_positions.resize(200);
std::mt19937 gen(42);
std::uniform_int_distribution<size_t> position_generator(0, 1000 - 1);
for (size_t i = 0; i < access_positions.size(); ++i)
access_positions[i] = position_generator(gen);
if constexpr (std::is_same_v<tag_t, baseline_tag>)
{
std::vector<seqan3::aa27_vector> translated_aa_sequences = dna_sequence_collection
| seqan3::views::translate_join
| seqan3::views::to<std::vector<seqan3::aa27_vector>>;
random_access_impl(state, translated_aa_sequences, access_positions);
}
else
{
auto translated_aa_view = dna_sequence_collection | seqan3::views::translate_join;
random_access_impl(state, translated_aa_view, access_positions);
}
}
BENCHMARK_TEMPLATE(random_access, baseline_tag);
BENCHMARK_TEMPLATE(random_access, translate_join_tag);
// ============================================================================
// run
// ============================================================================
BENCHMARK_MAIN();
|
