SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t > Class Template Reference

A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet. More...

#include <seqan3/alphabet/structure/structured_aa.hpp>

+ Inheritance diagram for seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >:

Public Types

using char_type = alphabet_char_t< sequence_alphabet_type >
 Equals the char_type of sequence_alphabet_type.
 
using sequence_alphabet_type = sequence_alphabet_t
 First template parameter as member type.
 
using structure_alphabet_type = structure_alphabet_t
 Second template parameter as member type.
 

Public Member Functions

Constructors, destructor and assignment
constexpr structured_aa () noexcept=default
 Defaulted.
 
constexpr structured_aa (structured_aa const &) noexcept=default
 Defaulted.
 
constexpr structured_aa (structured_aa &&) noexcept=default
 Defaulted.
 
constexpr structured_aaoperator= (structured_aa const &) noexcept=default
 Defaulted.
 
constexpr structured_aaoperator= (structured_aa &&) noexcept=default
 Defaulted.
 
 ~structured_aa () noexcept=default
 Defaulted.
 
template<typename component_type >
constexpr structured_aa (component_type const alph)
 Construction via a value of one of the components.
 
template<typename indirect_component_type >
constexpr structured_aa (indirect_component_type const alph)
 Construction via a value of a subtype that is assignable to one of the components.
 
template<typename component_type >
constexpr structured_aaoperator= (component_type const alph)
 Assignment via a value of one of the components.
 
template<typename indirect_component_type >
constexpr structured_aaoperator= (indirect_component_type const alph)
 Assignment via a value of a subtype that is assignable to one of the components.
 
template<typename component_type >
requires (!std::derived_from<component_type, alphabet_tuple_base>) && is_unique_component<component_type>
constexpr derived_typeoperator= (component_type const alph) noexcept
 Inherit operators from base.
 
template<typename indirect_component_type >
requires ((!std::derived_from<indirect_component_type, alphabet_tuple_base>) && (!is_unique_component<indirect_component_type>) && (std::assignable_from<component_types, indirect_component_type> || ...))
constexpr derived_typeoperator= (indirect_component_type const alph) noexcept
 Inherit operators from base.
 
Write functions
constexpr structured_aaassign_char (char_type const c) noexcept
 Assign from a nucleotide character. This modifies the internal sequence letter.
 
Read functions
constexpr char_type to_char () const noexcept
 Return a character. This reads the internal sequence letter.
 
- Public Member Functions inherited from seqan3::alphabet_tuple_base< derived_type, component_types >
constexpr alphabet_tuple_base (component_types... components) noexcept
 Construction from initialiser-list.
 
template<typename component_type >
requires (!std::is_base_of_v<alphabet_tuple_base, component_type>) && is_unique_component<component_type>
constexpr alphabet_tuple_base (component_type const alph) noexcept
 Construction via a value of one of the components.
 
template<typename indirect_component_type >
requires ((detail::instantiate_if_v< detail::lazy<std::is_convertible, indirect_component_type, component_types>, detail::tuple_general_guard<derived_type, indirect_component_type, component_types...>> || ...))
constexpr alphabet_tuple_base (indirect_component_type const alph) noexcept
 Construction via a value of a subtype that is assignable to one of the components.
 
template<typename component_type >
requires (!std::derived_from<component_type, alphabet_tuple_base>) && is_unique_component<component_type>
constexpr derived_typeoperator= (component_type const alph) noexcept
 Assignment via a value of one of the components.
 
template<typename indirect_component_type >
requires ((!std::derived_from<indirect_component_type, alphabet_tuple_base>) && (!is_unique_component<indirect_component_type>) && (std::assignable_from<component_types, indirect_component_type> || ...))
constexpr derived_typeoperator= (indirect_component_type const alph) noexcept
 Assignment via a value of a subtype that is assignable to one of the components.
 
template<typename type >
requires is_unique_component<type>
constexpr operator type () const noexcept
 Implicit cast to a single letter. Works only if the type is unique in the type list.
 
- Public Member Functions inherited from seqan3::alphabet_base< derived_type,(1 *... *alphabet_size< component_types >), void >
constexpr alphabet_base () noexcept=default
 Defaulted.
 
constexpr alphabet_base (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_base (alphabet_base &&) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (alphabet_base &&) noexcept=default
 Defaulted.
 
 ~alphabet_base () noexcept=default
 Defaulted.
 
constexpr char_type to_char () const noexcept
 Return the letter as a character of char_type.
 
constexpr rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet).
 
constexpr derived_type & assign_char (char_type const chr) noexcept
 Assign from a character, implicitly converts invalid characters.
 
constexpr derived_type & assign_rank (rank_type const c) noexcept
 Assign from a numeric value.
 

Static Public Member Functions

static constexpr bool char_is_valid (char_type const c) noexcept
 Validate whether a character is valid in the sequence alphabet.
 

Private Types

using base_type = alphabet_tuple_base< structured_aa< sequence_alphabet_t, structure_alphabet_t >, sequence_alphabet_t, structure_alphabet_t >
 The base type.
 

Related Symbols

(Note that these are not member symbols.)

template<typename sequence_alphabet_type , typename structure_alphabet_type >
 structured_aa (sequence_alphabet_type &&, structure_alphabet_type &&) -> structured_aa< std::decay_t< sequence_alphabet_type >, std::decay_t< structure_alphabet_type > >
 Type deduction guide enables usage of structured_aa without specifying template args.
 

Additional Inherited Members

- Static Public Attributes inherited from seqan3::alphabet_base< derived_type,(1 *... *alphabet_size< component_types >), void >
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.
 
- Protected Types inherited from seqan3::alphabet_base< derived_type,(1 *... *alphabet_size< component_types >), void >
using char_type = std::conditional_t< std::same_as< void, void >, char, void >
 The char representation; conditional needed to make semi alphabet definitions legal.
 
using rank_type = detail::min_viable_uint_t< size - 1 >
 The type of the alphabet when represented as a number (e.g. via to_rank()).
 

Detailed Description

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
requires (!std::is_reference_v<sequence_alphabet_t>) && (!std::is_reference_v<structure_alphabet_t>)
class seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >

A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet.

Template Parameters
sequence_alphabet_tType of the first aminoacid letter; must model seqan3::writable_alphabet, seqan3::aminoacid_alphabet and satisfy the requirements on arguments by seqan3::alphabet_tuple_base.
structure_alphabet_tTypes of further structure letters; must model seqan3::writable_alphabet and satisfy the requirements on arguments by seqan3::alphabet_tuple_base.

This composite pairs an aminoacid alphabet with a structure alphabet. The rank values correspond to numeric values in the size of the composite, while the character values are taken from the sequence alphabet and the structure annotation is taken from the structure alphabet.

As with all seqan3::alphabet_tuple_base s you may access the individual alphabet letters in regular c++ tuple notation, i.e. get<0>(t) and objects can be brace-initialized with the individual members.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
int main()
{
using namespace seqan3::literals;
using seqan3::get;
seqan3::debug_stream << seqan3::to_rank(letter) << ' ' // 199
<< seqan3::to_rank(get<0>(letter)) << ' ' // 22
<< seqan3::to_rank(get<1>(letter)) << '\n'; // 1
seqan3::debug_stream << seqan3::to_char(letter) << ' ' // W
<< seqan3::to_char(get<0>(letter)) << ' ' // W
<< seqan3::to_char(get<1>(letter)) << '\n'; // B
// Modify:
get<0>(letter) = 'V'_aa27;
seqan3::debug_stream << seqan3::to_char(letter) << '\n'; // V
}
Provides seqan3::aa27, container aliases and string literals.
A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet.
Definition structured_aa.hpp:52
Provides seqan3::debug_stream and related types.
Provides the dssp format for protein structure.
constexpr auto to_char
Return the char representation of an alphabet object.
Definition alphabet/concept.hpp:383
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition alphabet/concept.hpp:152
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
The SeqAn namespace for literals.
constexpr auto const & get(configuration< configs_t... > const &config) noexcept
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition configuration.hpp:412
Provides the composite of aminoacid with structure alphabets.

This seqan3::alphabet_tuple_base itself fulfills seqan3::alphabet.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Member Typedef Documentation

◆ char_type

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
using seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::char_type = alphabet_char_t<sequence_alphabet_type>

Equals the char_type of sequence_alphabet_type.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ sequence_alphabet_type

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
using seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::sequence_alphabet_type = sequence_alphabet_t

First template parameter as member type.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ structure_alphabet_type

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
using seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::structure_alphabet_type = structure_alphabet_t

Second template parameter as member type.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Constructor & Destructor Documentation

◆ structured_aa() [1/2]

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
template<typename component_type >
constexpr seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::structured_aa ( component_type const  alph)
inlineconstexpr

Construction via a value of one of the components.

See also
seqan3::alphabet_tuple_base::alphabet_tuple_base(component_type const alph)

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ structured_aa() [2/2]

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
template<typename indirect_component_type >
constexpr seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::structured_aa ( indirect_component_type const  alph)
inlineconstexpr

Construction via a value of a subtype that is assignable to one of the components.

See also
seqan3::alphabet_tuple_base::alphabet_tuple_base(indirect_component_type const alph)

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Member Function Documentation

◆ assign_char()

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
constexpr structured_aa & seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::assign_char ( char_type const  c)
inlineconstexprnoexcept

Assign from a nucleotide character. This modifies the internal sequence letter.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ char_is_valid()

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
static constexpr bool seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::char_is_valid ( char_type const  c)
inlinestaticconstexprnoexcept

Validate whether a character is valid in the sequence alphabet.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ operator=() [1/4]

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
template<typename component_type >
constexpr structured_aa & seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::operator= ( component_type const  alph)
inlineconstexpr

Assignment via a value of one of the components.

See also
seqan3::alphabet_tuple_base::operator=(component_type const alph)

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ operator=() [2/4]

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
template<typename component_type >
requires (!std::derived_from<component_type, alphabet_tuple_base>) && is_unique_component<component_type>
constexpr derived_type & seqan3::alphabet_tuple_base< derived_type, component_types >::operator= ( component_type const  alph)
inlineconstexprnoexcept

Inherit operators from base.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ operator=() [3/4]

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
template<typename indirect_component_type >
constexpr structured_aa & seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::operator= ( indirect_component_type const  alph)
inlineconstexpr

Assignment via a value of a subtype that is assignable to one of the components.

See also
seqan3::alphabet_tuple_base::operator=(indirect_component_type const alph)

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ operator=() [4/4]

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
template<typename indirect_component_type >
requires ((!std::derived_from<indirect_component_type, alphabet_tuple_base>) && (!is_unique_component<indirect_component_type>) && (std::assignable_from<component_types, indirect_component_type> || ...))
constexpr derived_type & seqan3::alphabet_tuple_base< derived_type, component_types >::operator= ( indirect_component_type const  alph)
inlineconstexprnoexcept

Inherit operators from base.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ to_char()

template<writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
constexpr char_type seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >::to_char ( ) const
inlineconstexprnoexcept

Return a character. This reads the internal sequence letter.

This entity is experimental and subject to change in the future. Experimental since version 3.1.


The documentation for this class was generated from the following file:
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