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

#include <seqan3/alphabet/nucleotide/dna16sam.hpp>

Inheritance diagram for seqan3::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.

Public Member Functions inherited from seqan3::nucleotide_base< dna16sam, 16 >
constexpr	nucleotide_base (other_nucl_type const &other) noexcept
	Allow explicit construction from any other nucleotide type and convert via the character representation. More...

constexpr dna16sam	complement () const noexcept
	Return the complement of the letter. More...

Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t >
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. More...

constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet). More...

constexpr derived_type &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters. More...

constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value. More...

Related Functions
(Note that these are not member functions.)
using	dna16sam_vector = std::vector< dna16sam >
	Alias for an std::vector of seqan3::dna16sam. More...

Nucleotide literals
constexpr dna16sam	operator""_dna16sam (char const c) noexcept
	The seqan3::dna16sam char literal. More...

dna16sam_vector	operator""_dna16sam (char const *s, size_t n)
	The seqan3::dna16sam string literal. More...

Additional Inherited Members
Static Public Member Functions inherited from seqan3::nucleotide_base< dna16sam, 16 >
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. More...

Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t >
static constexpr detail::min_viable_uint_t< size >	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take. More...

Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t >
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. 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...

Detailed Description

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

The seqan3::dna16sam alphabet is the nucleotide alphabet used inside the SAM, BAM and CRAM formats. It has all the letters of the seqan3::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 seqan3::dna15) and unknown characters are silently converted to 'N'.

The complement is the same as for seqan3::dna15, with the addition that the complement of '=' is unknown and therefore set to 'N'.

#include <seqan3/alphabet/nucleotide/dna16sam.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna16sam letter{'A'_dna16sam};
 
    letter.assign_char('=');
    seqan3::debug_stream << letter << '\n'; // prints "="
 
    letter.assign_char('F'); // Unknown characters are implicitly converted to N.
    seqan3::debug_stream << letter << '\n'; // "N";
}

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

◆ dna16sam_vector

using dna16sam_vector = std::vector<dna16sam>

This entity is stable. Since version 3.1.

◆ operator""_dna16sam() [1/2]

dna16sam_vector operator""_dna16sam	(	char const *	s,
		size_t	n
	)

Returns: seqan3::dna16sam_vector

Parameters

[in]	s	The string literal to assign from.
[in]	n	The length of the string literal s.

You can use this string literal to easily assign to seqan3::dna16sam_vector:

// generated from test/snippet/alphabet/nucleotide/@target_alphabet@_literal.cpp.in
 
#include <seqan3/alphabet/nucleotide/dna16sam.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna16sam_vector sequence1{"ACGTTA"_dna16sam};
    seqan3::dna16sam_vector sequence2 = "ACGTTA"_dna16sam;
    auto sequence3 = "ACGTTA"_dna16sam;
}

This entity is stable. Since version 3.1.

◆ operator""_dna16sam() [2/2]

constexpr dna16sam operator""_dna16sam ( char const c )

Returns: seqan3::dna16sam

Parameters

[in] c The character to assign from.

You can use this char literal to assign a seqan3::dna16sam character:

// generated from test/snippet/alphabet/nucleotide/@target_alphabet@_char_literal.cpp.in
 
#include <seqan3/alphabet/nucleotide/dna16sam.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna16sam letter1{'A'_dna16sam};
    auto letter2 = 'A'_dna16sam;
}

This entity is stable. Since version 3.1.

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

seqan3/alphabet/nucleotide/dna16sam.hpp

Public Member Functions

Related Functions

Additional Inherited Members

Detailed Description

Friends And Related Function Documentation

◆ dna16sam_vector

◆ operator""_dna16sam() [1/2]

◆ operator""_dna16sam() [2/2]