seqan3::sam_dna16 Class Reference

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

#include <seqan3/alphabet/nucleotide/sam_dna16.hpp>

Inheritance diagram for seqan3::sam_dna16:

Public Member Functions
Constructors, destructor and assignment
constexpr	sam_dna16 () noexcept=default
	Defaulted.
constexpr	sam_dna16 (sam_dna16 const &) noexcept=default
	Defaulted.
constexpr	sam_dna16 (sam_dna16 &&) noexcept=default
	Defaulted.
constexpr sam_dna16 &	operator= (sam_dna16 const &) noexcept=default
	Defaulted.
constexpr sam_dna16 &	operator= (sam_dna16 &&) noexcept=default
	Defaulted.
	~sam_dna16 () noexcept=default
	Defaulted.
Read functions
constexpr sam_dna16	complement () const noexcept
	Return the complement of the letter. More...
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 derived_type &	assign_char (char_type const c) 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...

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. More...

Static Public Attributes
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
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. 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 = nucleotide_base< sam_dna16, 16 >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::nucleotide_base.
friend	derived_type
	Befriend the derived_type so it can instantiate.
rank_type	rank {}
	The value of the alphabet letter is stored as the rank.

Static Private Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank
	Char to value conversion table. More...
static const std::array< sam_dna16, alphabet_size >	complement_table
	The complement table. More...
static constexpr char_type	rank_to_char [alphabet_size]
	The representation is the same as in the SAM specifications (which is NOT in alphabetical order). More...
static constexpr std::array< bool, 256 >	valid_char_table
	Implementation of char_is_valid().

Related Functions
(Note that these are not member functions.)
using	sam_dna16_vector = std::vector< sam_dna16 >
	Alias for an std::vector of seqan3::sam_dna16.
Literals
constexpr sam_dna16	operator""_sam_dna16 (char const c) noexcept
	The seqan3::sam_dna16 char literal. More...
sam_dna16_vector	operator""_sam_dna16 (char const *s, size_t n)
	The seqan3::sam_dna16 string literal. More...
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

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

The seqan3::sam_dna16 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 sam_dna16 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/sam_dna16.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_sam_dna16;
 
    seqan3::sam_dna16 my_letter{'A'_sam_dna16};
 
    my_letter.assign_char('=');
 
    my_letter.assign_char('F'); // unknown characters are implicitly converted to N.
    seqan3::debug_stream << my_letter << '\n'; // "N";
}

Member Typedef Documentation

char_type

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

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

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

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

using seqan3::alphabet_base< derived_type, size, char_t >::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()

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

constexpr derived_type& seqan3::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 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()

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

constexpr derived_type& seqan3::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 seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

char_is_valid()

static constexpr bool seqan3::nucleotide_base< sam_dna16 , 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 seqan3::semialphabet::char_is_valid_for() requirement via the seqan3::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 seqan3::dna4, because its informational content is identical to 'T'.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

complement()

constexpr sam_dna16 seqan3::nucleotide_base< sam_dna16 , size >::complement ( ) const

inlineconstexprnoexceptinherited

Return the complement of the letter.

See Nucleotide for the actual values.

Provides an implementation for seqan3::complement, required to model seqan3::nucleotide_alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_char()

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

constexpr char_type seqan3::alphabet_base< derived_type, size, char_t >::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()

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

constexpr rank_type seqan3::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 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

operator""_sam_dna16() [1/2]

sam_dna16_vector operator""_sam_dna16 ( char const *  s, size_t  n  )

related

The seqan3::sam_dna16 string literal.

Returns

seqan3::sam_dna16_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::sam_dna16_vector:

#include <seqan3/alphabet/nucleotide/sam_dna16.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_sam_dna16;
    
    seqan3::sam_dna16_vector foo{"ACgtTA"_sam_dna16};
    seqan3::sam_dna16_vector bar = "ACG==A"_sam_dna16;
    auto bax = "A=GTT!"_sam_dna16;
 
    seqan3::debug_stream << foo << "\n" << bar << "\n" << bax << "\n";
}

operator""_sam_dna16() [2/2]

constexpr sam_dna16 operator""_sam_dna16 ( char const  c )

related

The seqan3::sam_dna16 char literal.

Returns

seqan3::sam_dna16

Parameters

[in]

c

The character to assign from.

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

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

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< derived_type, size, char_t >::alphabet_size = 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.

char_to_rank

constexpr std::array<rank_type, 256> seqan3::sam_dna16::char_to_rank

staticconstexprprivate

Initial value:

{
        [] () constexpr
        {
            std::array<rank_type, 256> ret{};
 
            
            for (auto & c : ret)
                c = 15; 
 
            
            for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
            {
                ret[         rank_to_char[rnk] ] = rnk;
                ret[to_lower(rank_to_char[rnk])] = rnk;
            }
 
            
            ret['U'] = ret['T']; ret['u'] = ret['t'];
 
            return ret;
        }()
    }

Char to value conversion table.

complement_table

constexpr std::array< sam_dna16, sam_dna16::alphabet_size > seqan3::sam_dna16::complement_table

staticconstexprprivate

Initial value:

{
    'N'_sam_dna16,    
    'T'_sam_dna16,    
    'G'_sam_dna16,    
    'K'_sam_dna16,    
    'C'_sam_dna16,    
    'Y'_sam_dna16,    
    'S'_sam_dna16,    
    'B'_sam_dna16,    
    'A'_sam_dna16,    
    'W'_sam_dna16,    
    'R'_sam_dna16,    
    'D'_sam_dna16,    
    'M'_sam_dna16,    
    'H'_sam_dna16,    
    'V'_sam_dna16,    
    'N'_sam_dna16     
}

The complement table.

rank_to_char

constexpr char_type seqan3::sam_dna16::rank_to_char[alphabet_size]

staticconstexprprivate

Initial value:

{
        '=',
        'A',
        'C',
        'M',
        'G',
        'R',
        'S',
        'V',
        'T',
        'W',
        'Y',
        'H',
        'K',
        'D',
        'B',
        'N'
    }

The representation is the same as in the SAM specifications (which is NOT in alphabetical order).

---

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

• seqan3/alphabet/nucleotide/sam_dna16.hpp