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aa27.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 aa27 : public aminoacid_base<aa27, 27>
{
private:
using base_t = aminoacid_base<aa27, 27>;
friend base_t;
friend base_t::base_t;
public:
constexpr aa27() noexcept = default;
constexpr aa27(aa27 const &) noexcept = default;
constexpr aa27(aa27 &&) noexcept = default;
constexpr aa27 & operator=(aa27 const &) noexcept = default;
constexpr aa27 & operator=(aa27 &&) noexcept = default;
~aa27() noexcept = default;
using base_t::base_t;
private:
static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R',
'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', '*'};
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 'X' (UNKNOWN)
ret.fill(23u);
// 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;
}
return ret;
}()};
};
// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------
using aa27_vector = std::vector<aa27>;
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
inline namespace literals
{
constexpr aa27 operator""_aa27(char const c) noexcept
{
return aa27{}.assign_char(c);
}
SEQAN3_WORKAROUND_LITERAL aa27_vector operator""_aa27(char const * const s, size_t const n)
{
aa27_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::aa27::aa27
constexpr aa27() noexcept=default
Defaulted.
seqan3::aa27::aa27_vector
std::vector< aa27 > aa27_vector
Alias for a std::vector of seqan3::aa27.
Definition aa27.hpp:117
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< aa27, 27 >::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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