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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 <ranges>
#include <stdexcept>
#include <string_view>
#include <type_traits>
#include <utility>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alphabet/gap/gapped.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/views/to_char.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include <seqan3/test/expect_same_type.hpp>
#include <seqan3/utility/tuple/concept.hpp>
using seqan3::operator""_dna4;
template <typename t>
struct align_pairwise_test : ::testing::Test
{
// two helper variables to check if the TypeParam contains vectorised.
using dummy_cfg_t = std::conditional_t<std::is_same_v<void, t>, decltype(seqan3::align_cfg::min_score{-1}), t>;
using config_t = decltype(seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme | dummy_cfg_t{});
static constexpr bool is_vectorised = config_t::template exists<seqan3::align_cfg::vectorised>();
};
using testing_types = ::testing::Types<void, seqan3::align_cfg::parallel>;
TYPED_TEST_SUITE(align_pairwise_test, testing_types, );
template <typename type_param_t, typename seq_t, typename cfg_t>
auto call_alignment(seq_t && seq, cfg_t && cfg)
{
if constexpr (std::same_as<type_param_t, void>)
{
return seqan3::align_pairwise(std::forward<seq_t>(seq), std::forward<cfg_t>(cfg));
}
else if constexpr (std::same_as<type_param_t, seqan3::align_cfg::parallel>)
{
auto && config = cfg | seqan3::align_cfg::parallel{4};
return seqan3::align_pairwise(std::forward<seq_t>(seq), std::forward<decltype(config)>(config));
}
}
TYPED_TEST(align_pairwise_test, single_pair)
{
using namespace std::literals;
auto seq1 = "ACGTGATG"_dna4;
auto seq2 = "AGTGATACT"_dna4;
// use std::tie
auto p1 = std::tie(seq1, seq2);
{ // the score
seqan3::configuration cfg =
seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme | seqan3::align_cfg::output_score{};
for (auto && res : call_alignment<TypeParam>(p1, cfg))
{
EXPECT_EQ(res.score(), -4.0);
}
}
{ // with everything (default if no output is specified)
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
unsigned idx = 0;
for (auto && res : call_alignment<TypeParam>(p1, cfg))
{
EXPECT_EQ(res.sequence1_id(), idx);
EXPECT_EQ(res.sequence2_id(), idx++);
EXPECT_EQ(res.score(), -4);
EXPECT_EQ(res.sequence1_end_position(), 8u);
EXPECT_EQ(res.sequence2_end_position(), 9u);
auto && [gap1, gap2] = res.alignment();
EXPECT_RANGE_EQ(gap1 | seqan3::views::to_char, "ACGTGATG--"sv);
EXPECT_RANGE_EQ(gap2 | seqan3::views::to_char, "A-GTGATACT"sv);
}
}
// use std::pair
std::pair sequences{"ACGTGATG"_dna4, "AGTGATACT"_dna4};
{ // the score
seqan3::configuration cfg =
seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme | seqan3::align_cfg::output_score{};
for (auto && res : call_alignment<TypeParam>(sequences, cfg))
{
EXPECT_EQ(res.score(), -4.0);
}
}
{ // with everything (default if no output is specified)
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
unsigned idx = 0;
for (auto && res : call_alignment<TypeParam>(sequences, cfg))
{
EXPECT_EQ(res.sequence1_id(), idx);
EXPECT_EQ(res.sequence2_id(), idx++);
EXPECT_EQ(res.score(), -4);
EXPECT_EQ(res.sequence1_end_position(), 8u);
EXPECT_EQ(res.sequence2_end_position(), 9u);
auto && [gap1, gap2] = res.alignment();
EXPECT_RANGE_EQ(gap1 | seqan3::views::to_char, "ACGTGATG--"sv);
EXPECT_RANGE_EQ(gap2 | seqan3::views::to_char, "A-GTGATACT"sv);
}
}
// use make_pair
auto p2 = std::make_pair(seq1, seq2);
{ // the score
seqan3::configuration cfg =
seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme | seqan3::align_cfg::output_score{};
for (auto && res : call_alignment<TypeParam>(p2, cfg))
{
EXPECT_EQ(res.score(), -4.0);
}
}
{ // with everything (default if no output is specified)
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
unsigned idx = 0;
for (auto && res : call_alignment<TypeParam>(p2, cfg))
{
EXPECT_EQ(res.sequence1_id(), idx);
EXPECT_EQ(res.sequence2_id(), idx++);
EXPECT_EQ(res.score(), -4);
EXPECT_EQ(res.sequence1_end_position(), 8u);
EXPECT_EQ(res.sequence2_end_position(), 9u);
auto && [gap1, gap2] = res.alignment();
EXPECT_RANGE_EQ(gap1 | seqan3::views::to_char, "ACGTGATG--"sv);
EXPECT_RANGE_EQ(gap2 | seqan3::views::to_char, "A-GTGATACT"sv);
}
}
}
TYPED_TEST(align_pairwise_test, single_pair_double_score)
{
using namespace std::literals;
if constexpr (!TestFixture::is_vectorised)
{ // not building for vectorised version.
auto seq1 = "ACGTGATG"_dna4;
auto seq2 = "AGTGATACT"_dna4;
auto p = std::tie(seq1, seq2);
{ // the score
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme
| seqan3::align_cfg::output_score{} | seqan3::align_cfg::score_type<double>{};
for (auto && res : call_alignment<TypeParam>(p, cfg))
{
EXPECT_EQ(res.score(), -4.0);
EXPECT_SAME_TYPE(decltype(res.score()), double);
}
}
{ // with everything (default if no output is specified)
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme
| seqan3::align_cfg::output_alignment{} | seqan3::align_cfg::output_end_position{}
| seqan3::align_cfg::output_sequence1_id{}
| seqan3::align_cfg::output_sequence2_id{} | seqan3::align_cfg::output_score{}
| seqan3::align_cfg::score_type<double>{};
for (auto && res : call_alignment<TypeParam>(p, cfg))
{
EXPECT_EQ(res.score(), -4);
EXPECT_EQ(res.sequence1_end_position(), 8u);
EXPECT_EQ(res.sequence2_end_position(), 9u);
auto && [gap1, gap2] = res.alignment();
EXPECT_RANGE_EQ(gap1 | seqan3::views::to_char, "ACGTGATG--"sv);
EXPECT_RANGE_EQ(gap2 | seqan3::views::to_char, "A-GTGATACT"sv);
}
}
}
}
TYPED_TEST(align_pairwise_test, single_view)
{
using namespace std::literals;
auto seq1 = "ACGTGATG"_dna4;
auto seq2 = "AGTGATACT"_dna4;
auto v = std::views::single(std::tie(seq1, seq2)) | std::views::common;
{ // the score
seqan3::configuration cfg =
seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme | seqan3::align_cfg::output_score{};
for (auto && res : call_alignment<TypeParam>(v, cfg))
{
EXPECT_EQ(res.score(), -4);
}
}
{ // with everything (default if no output is specified)
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
for (auto && res : call_alignment<TypeParam>(v, cfg))
{
EXPECT_EQ(res.score(), -4);
auto && [gap1, gap2] = res.alignment();
EXPECT_RANGE_EQ(gap1 | seqan3::views::to_char, "ACGTGATG--"sv);
EXPECT_RANGE_EQ(gap2 | seqan3::views::to_char, "A-GTGATACT"sv);
}
}
}
TYPED_TEST(align_pairwise_test, collection)
{
using namespace std::literals;
auto seq1 = "ACGTGATG"_dna4;
auto seq2 = "AGTGATACT"_dna4;
auto p = std::tie(seq1, seq2);
std::vector<decltype(p)> vec{10, p};
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme
| seqan3::align_cfg::output_score{} | seqan3::align_cfg::output_alignment{};
for (auto && res : call_alignment<TypeParam>(vec, cfg))
{
EXPECT_EQ(res.score(), -4);
auto && [gap1, gap2] = res.alignment();
EXPECT_RANGE_EQ(gap1 | seqan3::views::to_char, "ACGTGATG--"sv);
EXPECT_RANGE_EQ(gap2 | seqan3::views::to_char, "A-GTGATACT"sv);
}
}
TYPED_TEST(align_pairwise_test, collection_with_double_score_type)
{
using namespace std::literals;
if constexpr (!TestFixture::is_vectorised)
{
auto seq1 = "ACGTGATG"_dna4;
auto seq2 = "AGTGATACT"_dna4;
auto p = std::tie(seq1, seq2);
std::vector<decltype(p)> vec{10, p};
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme
| seqan3::align_cfg::output_alignment{} | seqan3::align_cfg::output_score{}
| seqan3::align_cfg::score_type<double>{};
for (auto && res : call_alignment<TypeParam>(vec, cfg))
{
EXPECT_EQ(res.score(), -4);
auto && [gap1, gap2] = res.alignment();
EXPECT_RANGE_EQ(gap1 | seqan3::views::to_char, "ACGTGATG--"sv);
EXPECT_RANGE_EQ(gap2 | seqan3::views::to_char, "A-GTGATACT"sv);
}
}
}
TYPED_TEST(align_pairwise_test, bug_1598)
{
// https://github.com/seqan/seqan3/issues/1598
using seqan3::operator""_dna4;
auto s1 = "TTACGTACGGACTAGCTACAACATTACGGACTAC"_dna4;
auto g = "GGACGACATGACGTACGACTTTACGTACGACTAGC"_dna4;
auto s2 = g | std::views::drop(2);
// Configure the alignment kernel.
seqan3::configuration cfg = seqan3::align_cfg::method_global{}
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{}}
| seqan3::align_cfg::output_alignment{};
// Invoke the pairwise alignment which returns a lazy range over alignment results.
auto results = seqan3::align_pairwise(std::tie(s1, s2), cfg);
}
TEST(align_pairwise_test, parallel_without_parameter)
{
auto seq1 = "ACGTGATG"_dna4;
auto seq2 = "AGTGATACT"_dna4;
seqan3::configuration cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme
| seqan3::align_cfg::output_score{} | seqan3::align_cfg::parallel{};
EXPECT_THROW(seqan3::align_pairwise(std::tie(seq1, seq2), cfg), std::runtime_error);
}
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