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aa20.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 <vector>
#include <seqan3/alphabet/aminoacid/aminoacid_base.hpp>
#include <seqan3/alphabet/aminoacid/concept.hpp>
#include <seqan3/utility/char_operations/transform.hpp>
namespace seqan3
{
class aa20 : public aminoacid_base<aa20, 20>
{
private:
using base_t = aminoacid_base<aa20, 20>;
friend base_t;
friend base_t::base_t;
public:
constexpr aa20() noexcept = default;
constexpr aa20(aa20 const &) noexcept = default;
constexpr aa20(aa20 &&) noexcept = default;
constexpr aa20 & operator=(aa20 const &) noexcept = default;
constexpr aa20 & operator=(aa20 &&) noexcept = default;
~aa20() noexcept = default;
using base_t::base_t;
private:
static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L',
'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'};
static constexpr char_type rank_to_char(rank_type const rank)
{
return rank_to_char_table[rank];
}
static constexpr rank_type char_to_rank(char_type const chr)
{
using index_t = std::make_unsigned_t<char_type>;
return char_to_rank_table[static_cast<index_t>(chr)];
}
static constexpr std::array<rank_type, 256> char_to_rank_table{
[]() constexpr
{
std::array<rank_type, 256> ret{};
// initialize with 'S' because that appears most frequently
ret.fill(15u);
// reverse mapping for characters and their lowercase
for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
{
ret[static_cast<rank_type>(rank_to_char_table[rnk])] = rnk;
ret[static_cast<rank_type>(to_lower(rank_to_char_table[rnk]))] = rnk;
}
ret['B'] = ret['D'];
ret['b'] = ret['D']; // Convert b (either D/N) to D, since D occurs more frequently.
ret['J'] = ret['L'];
ret['j'] = ret['L']; // Convert j (either I/L) to L, since L occurs more frequently.
ret['O'] = ret['L'];
ret['o'] = ret['L']; // Convert Pyrrolysine to lysine.
ret['U'] = ret['C'];
ret['u'] = ret['C']; // Convert Selenocysteine to cysteine.
ret['X'] = ret['S'];
ret['x'] = ret['S']; // Convert unknown amino acids to serine.
ret['Z'] = ret['E'];
ret['z'] = ret['E']; // Convert z (either E/Q) to E, since E occurs more frequently.
ret['*'] = ret['W']; // The most common stop codon is UGA. This is most similar to a Tryptophan.
return ret;
}()};
};
// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------
using aa20_vector = std::vector<aa20>;
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
inline namespace literals
{
constexpr aa20 operator""_aa20(char const c) noexcept
{
return aa20{}.assign_char(c);
}
SEQAN3_WORKAROUND_LITERAL aa20_vector operator""_aa20(char const * const s, size_t const n)
{
aa20_vector r;
r.resize(n);
for (size_t i = 0; i < n; ++i)
r[i].assign_char(s[i]);
return r;
}
} // namespace literals
} // namespace seqan3
concept.hpp
Provides seqan3::aminoacid_alphabet.
aminoacid_base.hpp
Provides seqan3::aminoacid_base.
seqan3::aa20::aa20
constexpr aa20() noexcept=default
Defaulted.
seqan3::aa20::aa20_vector
std::vector< aa20 > aa20_vector
Alias for a std::vector of seqan3::aa20.
Definition aa20.hpp:147
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
seqan3::alphabet_base::rank_type
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition alphabet_base.hpp:77
seqan3::alphabet_base::alphabet_size
static constexpr detail::min_viable_uint_t< size > alphabet_size
The size of the alphabet, i.e. the number of different values it can take.
Definition alphabet_base.hpp:196
seqan3::alphabet_base::char_type
std::conditional_t< std::same_as< char_t, void >, char, char_t > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition alphabet_base.hpp:69
seqan3::aminoacid_base< aa20, 20 >::alphabet_size
static constexpr detail::min_viable_uint_t< size > alphabet_size
std::array::fill
T fill(T... args)
std::make_unsigned_t
seqan3::literals
The SeqAn namespace for literals.
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
seqan3::to_lower
constexpr char_type to_lower(char_type const c) noexcept
Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
Definition transform.hpp:74
SEQAN3_WORKAROUND_LITERAL
#define SEQAN3_WORKAROUND_LITERAL
Our char literals returning std::vector should be constexpr if constexpr std::vector is supported.
Definition platform.hpp:310
std::vector::resize
T resize(T... args)
transform.hpp
Provides utilities for modifying characters.
vector
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