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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: CC0-1.0
#include <utility>
#include <vector>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp>
#include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
#include <seqan3/alphabet/all.hpp>
#include <seqan3/core/debug_stream.hpp>
int main()
{
using namespace seqan3::literals;
std::vector vec{"MANLGYZW"_aa27, "LCKRLGNM"_aa27, "KPSKPRDYEDG"_aa27, "EQMCITQYR"_aa27};
using pair_t = decltype(std::tie(vec[0], vec[0]));
std::vector<pair_t> source;
for (unsigned i = 0; i < vec.size(); ++i)
{
for (unsigned j = i + 1; j < vec.size(); ++j)
{
source.push_back(std::tie(vec[i], vec[j]));
}
}
// Configure the alignment kernel.
auto config = seqan3::align_cfg::method_global{seqan3::align_cfg::free_end_gaps_sequence1_leading{false},
seqan3::align_cfg::free_end_gaps_sequence2_leading{true},
seqan3::align_cfg::free_end_gaps_sequence1_trailing{false},
seqan3::align_cfg::free_end_gaps_sequence2_trailing{true}}
| seqan3::align_cfg::scoring_scheme{seqan3::aminoacid_scoring_scheme{
seqan3::aminoacid_similarity_matrix::blosum62}}
| seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{-10},
seqan3::align_cfg::extension_score{-1}};
for (auto const & res : seqan3::align_pairwise(source, config))
seqan3::debug_stream << "Score: " << res.score() << '\n';
}
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