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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 <gtest/gtest.h>
#include <list>
#include <type_traits>
#include <utility>
#include <vector>
#include <seqan3/alignment/configuration/align_config_edit.hpp>
#include <seqan3/alignment/configuration/align_config_method.hpp>
#include <seqan3/alignment/configuration/align_config_output.hpp>
#include <seqan3/alignment/configuration/align_config_score_type.hpp>
#include <seqan3/alignment/pairwise/align_result_selector.hpp>
#include <seqan3/alphabet/gap/gapped.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/utility/tuple/concept.hpp>
#include <seqan3/utility/views/type_reduce.hpp>
struct alignment_selector_test : public ::testing::Test
{
using seq1_t = std::vector<seqan3::dna4>;
using seq2_t = std::list<seqan3::dna4>;
using gapped_seq1_t = seqan3::gap_decorator<seqan3::type_reduce_t<std::vector<seqan3::dna4> &>>;
using gapped_seq2_t = std::vector<seqan3::gapped<seqan3::dna4>>;
using alignment_t = std::tuple<gapped_seq1_t, gapped_seq2_t>;
template <typename config_t>
using alignment_result_value_t = typename seqan3::detail::align_result_selector<seq1_t, seq2_t, config_t>::type;
template <typename config_t>
using alignment_result_t = seqan3::alignment_result<alignment_result_value_t<config_t>>;
static constexpr seqan3::configuration base_config = []()
{
return seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
}();
};
TEST_F(alignment_selector_test, align_result_selector_all)
{
auto cfg = base_config | seqan3::align_cfg::output_score{} | seqan3::align_cfg::output_begin_position{}
| seqan3::align_cfg::output_end_position{} | seqan3::align_cfg::output_alignment{}
| seqan3::align_cfg::output_sequence1_id{} | seqan3::align_cfg::output_sequence2_id{};
using result_t = alignment_result_t<decltype(cfg)>;
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence1_id()), uint32_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence2_id()), uint32_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().score()), int32_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence1_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence2_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence1_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence2_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().alignment()), alignment_t const &>));
}
TEST_F(alignment_selector_test, align_result_selector_using_score_type)
{
auto cfg = seqan3::align_cfg::method_global{} | // TODO: Change to base_config once using_score_type has been fixed.
seqan3::align_cfg::edit_scheme | seqan3::align_cfg::output_score{}
| seqan3::align_cfg::output_end_position{} | seqan3::align_cfg::score_type<double>{};
using result_t = alignment_result_t<decltype(cfg)>;
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().score()), double>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence1_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence2_end_position()), size_t>));
}
TEST_F(alignment_selector_test, output_score_only)
{
auto cfg = base_config | seqan3::align_cfg::output_score{};
using result_t = alignment_result_t<decltype(cfg)>;
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().score()), int32_t>));
}
TEST_F(alignment_selector_test, output_end_positions_only)
{
auto cfg = base_config | seqan3::align_cfg::output_end_position{};
using result_t = alignment_result_t<decltype(cfg)>;
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence1_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence2_end_position()), size_t>));
}
TEST_F(alignment_selector_test, output_begin_positions_only)
{
auto cfg = base_config | seqan3::align_cfg::output_begin_position{};
using result_t = alignment_result_t<decltype(cfg)>;
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence1_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence2_begin_position()), size_t>));
}
TEST_F(alignment_selector_test, output_alignment_only)
{
auto cfg = base_config | seqan3::align_cfg::output_alignment{};
using result_t = alignment_result_t<decltype(cfg)>;
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().alignment()), alignment_t const &>));
}
TEST_F(alignment_selector_test, output_sequence1_id_only)
{
auto cfg = base_config | seqan3::align_cfg::output_sequence1_id{};
using result_t = alignment_result_t<decltype(cfg)>;
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence1_id()), uint32_t>));
}
TEST_F(alignment_selector_test, output_sequence2_id_only)
{
auto cfg = base_config | seqan3::align_cfg::output_sequence2_id{};
using result_t = alignment_result_t<decltype(cfg)>;
EXPECT_TRUE((std::is_same_v<decltype(std::declval<result_t>().sequence2_id()), uint32_t>));
}
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