seqan3::gap Class Reference

The alphabet of a gap character '-'. More...

#include <seqan3/alphabet/gap/gap.hpp>

Inheritance diagram for seqan3::gap:

Public Member Functions
Constructors, destructor and assignment
constexpr	gap () noexcept
	Defaulted.
constexpr	gap (gap const &)=default
	Defaulted.
constexpr	gap (gap &&)=default
	Defaulted.
constexpr gap &	operator= (gap const &)=default
	Defaulted.
constexpr gap &	operator= (gap &&)=default
	Defaulted.
	~gap ()=default
	Defaulted.
Read functions
constexpr char_type	to_char () const noexcept
	Return the letter as a character of char_type. More...
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet). More...
Write functions
constexpr gap &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...
constexpr gap &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value. More...

Static Public Attributes
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. More...

Protected Types
Member types
using	char_type = std::conditional_t< std::same_as< char, void >, char, char >
	The char representation; conditional needed to make semi alphabet definitions legal. More...
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()). More...

Private Types
using	base_t = alphabet_base< gap, 1, char >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::alphabet_base.
rank_type	rank
	The value of the alphabet letter is stored as the rank.

Static Private Attributes
static constexpr char	char_value = '-'
	The character that will be printed.

Related Functions
(Note that these are not member functions.)
Generic serialisation functions for all seqan3::semialphabet
All types that satisfy seqan3::semialphabet can be serialised via Cereal.
template<cereal_output_archive archive_t, semialphabet alphabet_t>
alphabet_rank_t< alphabet_t >	save_minimal (archive_t const &, alphabet_t const &l)
	Save an alphabet letter to stream. More...

Detailed Description

The alphabet of a gap character '-'.

The alphabet always has the same value ('-').

#include <iostream>
 
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    seqan3::gap my_gap = seqan3::gap{};
    seqan3::gap another_gap{};
    another_gap.assign_char('A'); // this does not change anything
 
    seqan3::debug_stream << my_gap.to_char(); // outputs '-'
    if (my_gap.to_char() == another_gap.to_char())
        seqan3::debug_stream << "Both gaps are the same!";
}

Member Typedef Documentation

char_type

using seqan3::alphabet_base< gap , size, char >::char_type = std::conditional_t<std::same_as<char , void>, char, char >

protectedinherited

The char representation; conditional needed to make semi alphabet definitions legal.

We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t is void.

This entity is stable. Since version 3.1.

rank_type

using seqan3::alphabet_base< gap , size, char >::rank_type = detail::min_viable_uint_t<size - 1>

protectedinherited

The type of the alphabet when represented as a number (e.g. via to_rank()).

This entity is stable. Since version 3.1.

Member Function Documentation

assign_char()

constexpr gap & seqan3::alphabet_base< gap , size, char >::assign_char ( char_type const  c )

inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters

c	The character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

assign_rank()

constexpr gap & seqan3::alphabet_base< gap , size, char >::assign_rank ( rank_type const  c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

to_char()

constexpr char_type seqan3::alphabet_base< gap , size, char >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

to_rank()

constexpr rank_type seqan3::alphabet_base< gap , size, char >::to_rank ( ) const

inlineconstexprnoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

save_minimal()

template<cereal_output_archive archive_t, semialphabet alphabet_t>

alphabet_rank_t< alphabet_t > save_minimal ( archive_t const &  , alphabet_t const &  l  )

related

Save an alphabet letter to stream.

Template Parameters

archive_t	Must satisfy seqan3::cereal_output_archive.
alphabet_t	Type of l; must satisfy seqan3::semialphabet.

Parameters

l	The alphabet letter.

Delegates to seqan3::to_rank.

Attention

These functions are never called directly, see the Alphabet module on how to use serialisation.

This entity is stable. Since version 3.1.

Member Data Documentation

alphabet_size

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< gap , size, char >::alphabet_size

staticconstexprinherited

The size of the alphabet, i.e. the number of different values it can take.

This entity is stable. Since version 3.1.

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

• seqan3/alphabet/gap/gap.hpp