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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 <seqan3/alignment/matrix/alignment_coordinate.hpp>
#include <seqan3/alignment/matrix/debug_matrix.hpp>
#include <seqan3/alignment/matrix/trace_directions.hpp>
namespace seqan3::test::alignment::fixture
{
static constexpr auto INF = std::nullopt;
static constexpr auto N = seqan3::detail::trace_directions::none;
static constexpr auto D = seqan3::detail::trace_directions::diagonal;
static constexpr auto u = seqan3::detail::trace_directions::up;
static constexpr auto l = seqan3::detail::trace_directions::left;
static constexpr auto U = seqan3::detail::trace_directions::up_open;
static constexpr auto L = seqan3::detail::trace_directions::left_open;
static constexpr auto DU = D | U;
static constexpr auto UL = U | L;
static constexpr auto DL = D | L;
static constexpr auto DUL = D | U | L;
static constexpr auto Du = D | u;
static constexpr auto Uu = U | u;
static constexpr auto uL = u | L;
static constexpr auto DuL = D | u | L;
static constexpr auto DUu = D | U | u;
static constexpr auto UuL = U | u | L;
static constexpr auto DUuL = D | U | u | L;
static constexpr auto Dl = D | l;
static constexpr auto Ul = U | l;
static constexpr auto DUl = D | U | l;
static constexpr auto Ll = L | l;
static constexpr auto DLl = D | L | l;
static constexpr auto ULl = U | L | l;
static constexpr auto DULl = D | U | L | l;
static constexpr auto ul = u | l;
static constexpr auto Dul = D | u | l;
static constexpr auto Uul = U | u | l ;
static constexpr auto DUul = D | U | u | l;
static constexpr auto uLl = u | L | l;
static constexpr auto DuLl = D | u | L | l;
static constexpr auto UuLl = U | u | L | l;
static constexpr auto DUuLl = D | U | u | L | l;
template <typename sequence1_t, typename sequence2_t, typename config_t, typename score_t,
typename score_vector_or_matrix_t, typename trace_vector_or_matrix_t>
struct alignment_fixture
{
sequence1_t sequence1;
sequence2_t sequence2;
config_t config;
score_t score;
std::string aligned_sequence1;
std::string aligned_sequence2;
seqan3::alignment_coordinate begin_positions;
seqan3::alignment_coordinate end_positions;
score_vector_or_matrix_t score_vector{};
trace_vector_or_matrix_t trace_vector{};
auto score_matrix() const requires seqan3::detail::matrix<score_vector_or_matrix_t>
{
return seqan3::detail::debug_matrix{score_vector};
};
auto score_matrix() const requires (!seqan3::detail::matrix<score_vector_or_matrix_t>)
{
seqan3::detail::row_wise_matrix<std::ranges::range_value_t<score_vector_or_matrix_t>>
score_matrix{seqan3::detail::number_rows{sequence2.size() + 1},
seqan3::detail::number_cols{sequence1.size() + 1},
score_vector};
return seqan3::detail::debug_matrix{std::move(score_matrix)};
};
auto trace_matrix() const requires seqan3::detail::matrix<trace_vector_or_matrix_t>
{
return seqan3::detail::debug_matrix{trace_vector};
};
auto trace_matrix() const requires (!seqan3::detail::matrix<trace_vector_or_matrix_t>)
{
seqan3::detail::row_wise_matrix<std::ranges::range_value_t<trace_vector_or_matrix_t>>
trace_matrix{seqan3::detail::number_rows{sequence2.size() + 1},
seqan3::detail::number_cols{sequence1.size() + 1},
trace_vector};
return seqan3::detail::debug_matrix{std::move(trace_matrix)};
};
};
template <typename sequence1_t, typename sequence2_t, typename config_t, typename score_t,
typename score_vector_or_matrix_t, typename trace_vector_or_matrix_t>
alignment_fixture(
sequence1_t sequence1,
sequence2_t sequence2,
config_t config,
score_t score,
std::string aligned_sequence1,
std::string aligned_sequence2,
seqan3::alignment_coordinate begin_positions,
seqan3::alignment_coordinate end_positions,
score_vector_or_matrix_t score_vector,
trace_vector_or_matrix_t trace_vector
)
-> alignment_fixture<sequence1_t, sequence2_t, config_t, score_t, score_vector_or_matrix_t, trace_vector_or_matrix_t>;
template <typename sequence1_t, typename sequence2_t, typename config_t, typename score_t>
alignment_fixture(
sequence1_t sequence1,
sequence2_t sequence2,
config_t config,
score_t score,
std::string aligned_sequence1,
std::string aligned_sequence2,
seqan3::alignment_coordinate begin_positions,
seqan3::alignment_coordinate end_positions
)
-> alignment_fixture<sequence1_t, sequence2_t, config_t, score_t,
std::vector<score_t>, std::vector<seqan3::detail::trace_directions>>;
template <typename config_t, typename alignment_fixture_t>
struct alignment_fixture_collection
{
config_t config;
std::vector<alignment_fixture_t> collection;
auto get_sequences() const
{
std::vector<decltype(collection[0].sequence1)> vec1;
std::vector<decltype(collection[0].sequence2)> vec2;
for (size_t i = 0; i < collection.size(); ++i)
{
vec1.push_back(collection[i].sequence1);
vec2.push_back(collection[i].sequence2);
}
return std::pair{vec1, vec2};
}
auto get_scores() const
{
std::vector<decltype(collection[0].score)> vec;
for (size_t i = 0; i < collection.size(); ++i)
vec.push_back(collection[i].score);
return vec;
}
auto get_end_positions() const
{
std::vector<decltype(collection[0].end_positions)> vec;
for (size_t i = 0; i < collection.size(); ++i)
vec.push_back(collection[i].end_positions);
return vec;
}
auto get_begin_positions() const
{
std::vector<decltype(collection[0].begin_positions)> vec;
for (size_t i = 0; i < collection.size(); ++i)
vec.push_back(collection[i].begin_positions);
return vec;
}
auto get_aligned_sequences1() const
{
std::vector<decltype(collection[0].aligned_sequence1)> vec;
for (size_t i = 0; i < collection.size(); ++i)
vec.push_back(collection[i].aligned_sequence1);
return vec;
}
auto get_aligned_sequences2() const
{
std::vector<decltype(collection[0].aligned_sequence2)> vec;
for (size_t i = 0; i < collection.size(); ++i)
vec.push_back(collection[i].aligned_sequence2);
return vec;
}
};
template <typename config_t, typename fixture_t>
alignment_fixture_collection(
config_t config,
std::vector<fixture_t> collection
)
-> alignment_fixture_collection<config_t, fixture_t>;
} // namespace seqan3::test::alignment::fixture
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