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nucleotide_scoring_scheme.hpp
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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
#pragma once
#include <seqan3/alignment/scoring/scoring_scheme_base.hpp>
#include <seqan3/alphabet/nucleotide/dna15.hpp>
namespace seqan3
{
template <arithmetic score_type = int8_t>
class nucleotide_scoring_scheme : public scoring_scheme_base<nucleotide_scoring_scheme<score_type>, dna15, score_type>
{
private:
using base_t = scoring_scheme_base<nucleotide_scoring_scheme, dna15, score_type>;
friend base_t;
public:
using typename base_t::matrix_type;
constexpr nucleotide_scoring_scheme() noexcept = default;
template <arithmetic score_arg_t>
constexpr nucleotide_scoring_scheme(match_score<score_arg_t> const ms, mismatch_score<score_arg_t> const mms) :
base_t{ms, mms}
{}
constexpr nucleotide_scoring_scheme(matrix_type const & matrix) noexcept : base_t{matrix}
{}
};
nucleotide_scoring_scheme() -> nucleotide_scoring_scheme<int8_t>;
template <arithmetic score_arg_type>
nucleotide_scoring_scheme(match_score<score_arg_type>,
mismatch_score<score_arg_type>) -> nucleotide_scoring_scheme<int8_t>;
template <arithmetic score_arg_type>
nucleotide_scoring_scheme(std::array<std::array<score_arg_type, 15>, 15>) -> nucleotide_scoring_scheme<score_arg_type>;
} // namespace seqan3
std::array
seqan3::nucleotide_scoring_scheme::nucleotide_scoring_scheme
nucleotide_scoring_scheme(std::array< std::array< score_arg_type, 15 >, 15 >) -> nucleotide_scoring_scheme< score_arg_type >
Deduce the score type from the provided matrix.
seqan3::nucleotide_scoring_scheme::nucleotide_scoring_scheme
constexpr nucleotide_scoring_scheme(matrix_type const &matrix) noexcept
Constructor for a custom scheme (delegates to set_custom_matrix()).
Definition nucleotide_scoring_scheme.hpp:60
seqan3::nucleotide_scoring_scheme::nucleotide_scoring_scheme
constexpr nucleotide_scoring_scheme() noexcept=default
The default constructor (delegates to set_hamming_distance()).
seqan3::nucleotide_scoring_scheme::nucleotide_scoring_scheme
nucleotide_scoring_scheme() -> nucleotide_scoring_scheme< int8_t >
Default constructed objects deduce to int8_t.
seqan3::nucleotide_scoring_scheme::nucleotide_scoring_scheme
nucleotide_scoring_scheme(match_score< score_arg_type >, mismatch_score< score_arg_type >) -> nucleotide_scoring_scheme< int8_t >
Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_...
seqan3::scoring_scheme_base< nucleotide_scoring_scheme< int8_t >, dna15, int8_t >::scoring_scheme_base
constexpr scoring_scheme_base(scoring_scheme_base const &) noexcept=default
seqan3::scoring_scheme_base< nucleotide_scoring_scheme, dna15, score_type >::matrix_type
std::array< std::array< score_type, matrix_size >, matrix_size > matrix_type
Definition scoring_scheme_base.hpp:117
dna15.hpp
Provides seqan3::dna15, container aliases and string literals.
arithmetic
A type that satisfies std::is_arithmetic_v<t>.
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
scoring_scheme_base.hpp
Provides seqan3::scoring_scheme_base.
seqan3::match_score
A strong type of underlying type score_type that represents the score of two matching characters.
Definition scoring_scheme_base.hpp:38
seqan3::mismatch_score
A strong type of underlying type score_type that represents the score two different characters.
Definition scoring_scheme_base.hpp:63
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