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#include <seqan3/alignment/pairwise/all.hpp> // for seqan3::align_cfg and seqan3::align_pairwise
#include <seqan3/alignment/scoring/all.hpp> // for seqan3::aminoacid_scoring_scheme and
// seqan3::aminoacid_similarity_matrix
#include <seqan3/alphabet/aminoacid/aa27.hpp> // for seqan3::operator""_aa27
#include <seqan3/core/debug_stream.hpp>
using seqan3::operator""_aa27;
int main()
{
auto seq1 = "QFSEEILSDIYCWMLQCGQERAV"_aa27;
auto seq2 = "AFLPGWQEENKLSKIWMKDCGCLW"_aa27;
// Configure the alignment kernel.
auto config = seqan3::align_cfg::method_global{} |
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{-9},
seqan3::align_cfg::extension_score{-2}};
for (auto const & res : seqan3::align_pairwise(std::tie(seq1, seq2), config))
seqan3::debug_stream << "Score: " << res.score() << '\n';
}
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