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_aa &	operator= (structured_aa const &) noexcept=default
	Defaulted.

constexpr structured_aa &	operator= (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_aa &	operator= (component_type const alph)
	Assignment via a value of one of the components.

template<typename indirect_component_type >
constexpr structured_aa &	operator= (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_type &	operator= (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_type &	operator= (indirect_component_type const alph) noexcept
	Inherit operators from base.

Write functions
constexpr structured_aa &	assign_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_type &	operator= (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_type &	operator= (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_base &	operator= (alphabet_base const &) noexcept=default
	Defaulted.

constexpr alphabet_base &	operator= (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.

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_t	Type 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_t	Types 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
 
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/alphabet/structure/dssp9.hpp>
#include <seqan3/alphabet/structure/structured_aa.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
    using seqan3::get;
 
    seqan3::structured_aa<seqan3::aa27, seqan3::dssp9> letter{'W'_aa27, 'B'_dssp9};
 
    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
}

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:

structured_aa.hpp

Public Types

Public Member Functions

Static Public Member Functions

Related Symbols

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ char_type

◆ sequence_alphabet_type

◆ structure_alphabet_type

Constructor & Destructor Documentation

◆ structured_aa() [1/2]

◆ structured_aa() [2/2]

Member Function Documentation

◆ assign_char()

◆ char_is_valid()

◆ operator=() [1/4]

◆ operator=() [2/4]

◆ operator=() [3/4]

◆ operator=() [4/4]

◆ to_char()