bio::alphabet::dna16sam Class Reference

A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=').. More...

#include <bio/alphabet/nucleotide/dna16sam.hpp>

Inheritance diagram for bio::alphabet::dna16sam:

Public Member Functions
Constructors, destructor and assignment
constexpr	dna16sam () noexcept=default
	Defaulted.
constexpr	dna16sam (dna16sam const &) noexcept=default
	Defaulted.
constexpr	dna16sam (dna16sam &&) noexcept=default
	Defaulted.
constexpr dna16sam &	operator= (dna16sam const &) noexcept=default
	Defaulted.
constexpr dna16sam &	operator= (dna16sam &&) noexcept=default
	Defaulted.
	~dna16sam () noexcept=default
	Defaulted.
Read functions
constexpr dna16sam	complement () const noexcept
	Return the complement of the letter.
Read functions
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).
Write functions
constexpr derived_type &	assign_char (char_type const c) 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 value has a one-to-one mapping to an alphabet value.

Static Public Attributes
static constexpr size_t	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take.

Protected Types
Member types
using	char_type = std::conditional_t< std::same_as< char_t, void >, char, char_t >
	The char representation; conditional needed to make semi alphabet definitions legal.
using	rank_type = meta::detail::min_viable_uint_t< size - 1 >
	The type of the alphabet when represented as a number (e.g. via to_rank()).

Related Functions
(Note that these are not member functions.)
Literals
consteval dna16sam	operator""_dna16sam (char const c)
	The bio::alphabet::dna16sam char literal.
template<meta::detail::literal_buffer_string str>
constexpr std::vector< dna16sam >	operator""_dna16sam ()
	The bio::alphabet::dna16sam string literal.

Detailed Description

A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=').

.

The bio::alphabet::dna16sam alphabet is the nucleotide alphabet used inside the SAM, BAM and CRAM formats. It has all the letters of the bio::alphabet::dna15 alphabet and the extra alphabet character '=' which denotes a nucleotide character identical to the reference. Without the context of this reference sequence, no assumptions can be made about the actual value of '=' letter.

Note that you can assign 'U' as a character to dna16sam and it will silently be converted to 'T'. Lower case letters are accepted when assigning from char (just like bio::alphabet::dna15) and unknown characters are silently converted to 'N'.

The complement is the same as for bio::alphabet::dna15, with the addition that the complement of '=' is unknown and therefore set to 'N'.

The binary representation of an object of this type corresponds to the binary representation in BAM/CRAM.

#include <bio/alphabet/nucleotide/dna16sam.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::dna16sam my_letter{'A'_dna16sam};
 
    my_letter.assign_char('=');
 
    my_letter.assign_char('F'); // unknown characters are implicitly converted to N.
    fmt::print("{}\n", my_letter); // "N";
}

Member Function Documentation

assign_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type & bio::alphabet::base< derived_type, size, char_t >::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 bio::alphabet::assign_char_to, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

assign_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type & bio::alphabet::base< derived_type, size, char_t >::assign_rank ( rank_type const  c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

char_is_valid()

static constexpr bool bio::alphabet::nucleotide_base< dna16sam , size >::char_is_valid ( char_type const  c )

inlinestaticconstexprnoexceptinherited

Validate whether a character value has a one-to-one mapping to an alphabet value.

Satisfies the bio::alphabet::semialphabet::char_is_valid_for() requirement via the bio::alphabet::char_is_valid_for() wrapper.

Behaviour specific to nucleotides: True also for lower case letters that silently convert to their upper case and true also for U/T respectively, e.g. 'U' is a valid character for bio::alphabet::dna4, because its informational content is identical to 'T'.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

complement()

constexpr dna16sam bio::alphabet::nucleotide_base< dna16sam , size >::complement ( ) const

inlineconstexprnoexceptinherited

Return the complement of the letter.

See Nucleotide for the actual values.

Provides an implementation for bio::alphabet::complement, required to model bio::alphabet::nucleotide.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr char_type bio::alphabet::base< derived_type, size, char_t >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr rank_type bio::alphabet::base< derived_type, size, char_t >::to_rank ( ) const

inlineconstexprnoexceptinherited

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

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

Friends And Related Function Documentation

operator""_dna16sam() [1/2]

template<meta::detail::literal_buffer_string str>

constexpr std::vector< dna16sam > operator""_dna16sam ( )

related

The bio::alphabet::dna16sam string literal.

Returns

std::vector<bio::alphabet::dna16sam>

You can use this string literal to easily create a std::vector<bio::alphabet::dna16sam>:

#include <bio/alphabet/nucleotide/dna16sam.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    std::vector<bio::alphabet::dna16sam> foo = "ACG==A"_dna16sam;
    auto bar = "A=GTTC"_dna16sam;
 
    fmt::print("{}\n{}\n", foo, bar);
}

operator""_dna16sam() [2/2]

consteval dna16sam operator""_dna16sam ( char const  c )

related

The bio::alphabet::dna16sam char literal.

Returns

bio::alphabet::dna16sam

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

• bio/alphabet/nucleotide/dna16sam.hpp