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aa10li.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 aa10li : public aminoacid_base<aa10li, 10>
{
private:
using base_t = aminoacid_base<aa10li, 10>;
friend base_t;
friend base_t::base_t;
public:
constexpr aa10li() noexcept = default;
constexpr aa10li(aa10li const &) noexcept = default;
constexpr aa10li(aa10li &&) noexcept = default;
constexpr aa10li & operator=(aa10li const &) noexcept = default;
constexpr aa10li & operator=(aa10li &&) noexcept = default;
~aa10li() noexcept = default;
using base_t::base_t;
private:
static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'F', 'G', 'H', 'I', 'J', 'K', 'P'};
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 char_type rank_to_char(rank_type const rank)
{
return rank_to_char_table[rank];
}
static constexpr std::array<rank_type, 256> char_to_rank_table{
[]() constexpr
{
std::array<rank_type, 256> ret{};
// initialize with 'A' because S appears most frequently and gets converted to A in this alphabet
ret.fill(0u); // Value-initialisation of std::array does usually initialise. `fill` is explicit.
// 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['D'] = ret['B'];
ret['d'] = ret['B']; // Convert D to B (either D/N).
ret['E'] = ret['B'];
ret['e'] = ret['B']; // Convert E to B (either D/N).
ret['L'] = ret['J'];
ret['l'] = ret['J']; // Convert L to J (either I/L).
ret['M'] = ret['J'];
ret['m'] = ret['J']; // Convert M to J (either I/L).
ret['N'] = ret['H'];
ret['n'] = ret['H']; // Convert N to H.
ret['O'] = ret['K'];
ret['o'] = ret['K']; // Convert Pyrrolysine to K.
ret['Q'] = ret['B'];
ret['q'] = ret['B']; // Convert Q to B (either D/N).
ret['R'] = ret['K'];
ret['r'] = ret['K']; // Convert R to K.
ret['S'] = ret['A'];
ret['s'] = ret['A']; // Convert S to A.
ret['T'] = ret['A'];
ret['t'] = ret['A']; // Convert T to A.
ret['U'] = ret['C'];
ret['u'] = ret['C']; // Convert Selenocysteine to C.
ret['V'] = ret['I'];
ret['v'] = ret['I']; // Convert V to I.
ret['W'] = ret['F'];
ret['w'] = ret['F']; // Convert W to F.
ret['X'] = ret['A'];
ret['x'] = ret['A']; // Convert unknown amino acids to Alanine.
ret['Y'] = ret['F'];
ret['y'] = ret['F']; // Convert Y to F.
ret['Z'] = ret['B'];
ret['z'] = ret['B']; // Convert Z (either E/Q) to B (either D/N).
ret['*'] = ret['F']; // The most common stop codon is UGA. This is most similar to a Tryptophan which in
// this alphabet gets converted to Phenylalanine.
return ret;
}()};
};
// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------
using aa10li_vector = std::vector<aa10li>;
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
inline namespace literals
{
constexpr aa10li operator""_aa10li(char const c) noexcept
{
return aa10li{}.assign_char(c);
}
SEQAN3_WORKAROUND_LITERAL aa10li_vector operator""_aa10li(char const * const s, size_t const n)
{
aa10li_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::aa10li::aa10li_vector
std::vector< aa10li > aa10li_vector
Alias for a std::vector of seqan3::aa10li.
Definition aa10li.hpp:188
seqan3::aa10li::aa10li
constexpr aa10li() noexcept=default
Defaulted.
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< aa10li, 10 >::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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