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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
// -----------------------------------------------------------------------------------------------------
#pragma once
#include <gtest/gtest.h>
#include <seqan3/alignment/configuration/align_config_score_type.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/range/views/to_char.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include "fixture/alignment_fixture.hpp"
template <auto _fixture>
struct pairwise_alignment_fixture : public ::testing::Test
{
auto fixture() -> decltype(seqan3::test::alignment::fixture::alignment_fixture{*_fixture}) const &
{
return *_fixture;
}
};
template <typename fixture_t>
class pairwise_alignment_callback_test : public fixture_t
{};
TYPED_TEST_SUITE_P(pairwise_alignment_callback_test);
TYPED_TEST_P(pairwise_alignment_callback_test, score)
{
auto const & fixture = this->fixture();
seqan3::configuration align_cfg = fixture.config |
seqan3::align_cfg::output_score{} |
seqan3::align_cfg::on_result{[&] (auto && result)
{
EXPECT_EQ(result.score(), fixture.score);
}};
std::vector database = fixture.sequence1;
std::vector query = fixture.sequence2;
seqan3::align_pairwise(std::tie(database, query), align_cfg);
}
TYPED_TEST_P(pairwise_alignment_callback_test, end_positions)
{
auto const & fixture = this->fixture();
seqan3::configuration align_cfg = fixture.config |
seqan3::align_cfg::output_end_position{} |
seqan3::align_cfg::output_score{} |
seqan3::align_cfg::score_type<double>{} |
seqan3::align_cfg::on_result{[&] (auto && result)
{
EXPECT_EQ(result.score(), fixture.score);
EXPECT_TRUE((std::same_as<decltype(result.score()), double>));
EXPECT_EQ(result.sequence1_end_position(), fixture.end_positions.first);
EXPECT_EQ(result.sequence2_end_position(), fixture.end_positions.second);
}};
std::vector database = fixture.sequence1;
std::vector query = fixture.sequence2;
seqan3::align_pairwise(std::tie(database, query), align_cfg);
}
TYPED_TEST_P(pairwise_alignment_callback_test, begin_positions)
{
auto const & fixture = this->fixture();
seqan3::configuration align_cfg = fixture.config |
seqan3::align_cfg::output_begin_position{} |
seqan3::align_cfg::output_end_position{} |
seqan3::align_cfg::output_score{} |
seqan3::align_cfg::on_result{[&] (auto && result)
{
EXPECT_EQ(result.score(), fixture.score);
EXPECT_EQ(result.sequence1_end_position(), fixture.end_positions.first);
EXPECT_EQ(result.sequence2_end_position(), fixture.end_positions.second);
EXPECT_EQ(result.sequence1_begin_position(), fixture.begin_positions.first);
EXPECT_EQ(result.sequence2_begin_position(), fixture.begin_positions.second);
}};
std::vector database = fixture.sequence1;
std::vector query = fixture.sequence2;
seqan3::align_pairwise(std::tie(database, query), align_cfg);
}
TYPED_TEST_P(pairwise_alignment_callback_test, alignment)
{
auto const & fixture = this->fixture();
seqan3::configuration align_cfg = fixture.config |
seqan3::align_cfg::output_score{} |
seqan3::align_cfg::output_end_position{} |
seqan3::align_cfg::output_begin_position{} |
seqan3::align_cfg::output_alignment{} |
seqan3::align_cfg::on_result{[&] (auto && result)
{
EXPECT_EQ(result.score(), fixture.score);
EXPECT_EQ(result.sequence1_end_position(), fixture.end_positions.first);
EXPECT_EQ(result.sequence2_end_position(), fixture.end_positions.second);
EXPECT_EQ(result.sequence1_begin_position(), fixture.begin_positions.first);
EXPECT_EQ(result.sequence2_begin_position(), fixture.begin_positions.second);
auto && [gapped_database, gapped_query] = result.alignment();
EXPECT_RANGE_EQ(gapped_database | seqan3::views::to_char,
fixture.aligned_sequence1);
EXPECT_RANGE_EQ(gapped_query | seqan3::views::to_char,
fixture.aligned_sequence2);
}};
std::vector database = fixture.sequence1;
std::vector query = fixture.sequence2;
seqan3::align_pairwise(std::tie(database, query), align_cfg);
}
REGISTER_TYPED_TEST_SUITE_P(pairwise_alignment_callback_test, score, end_positions, begin_positions, alignment);
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