The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)). More...

#include <seqan3/alphabet/nucleotide/dna3bs.hpp>

Inheritance diagram for seqan3::dna3bs:

Public Member Functions
Constructors, destructor and assignment
constexpr	dna3bs () noexcept=default
	Defaulted.

constexpr	dna3bs (dna3bs const &) noexcept=default
	Defaulted.

constexpr	dna3bs (dna3bs &&) noexcept=default
	Defaulted.

constexpr dna3bs &	operator= (dna3bs const &) noexcept=default
	Defaulted.

constexpr dna3bs &	operator= (dna3bs &&) noexcept=default
	Defaulted.

	~dna3bs () noexcept=default
	Defaulted.

Read functions
constexpr dna3bs	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< dna3bs, 3 >
	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.

static const std::array< dna3bs, alphabet_size >	complement_table
	The complement table. More...

static constexpr char_type	rank_to_char [alphabet_size]
	Value to char conversion table. 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	dna3bs_vector = std::vector< dna3bs >
	Alias for an std::vector of seqan3::dna3bs.

Literals
constexpr dna3bs	operator""_dna3bs (char const c) noexcept
	The seqan3::dna3bs char literal. More...

dna3bs_vector	operator""_dna3bs (char const *s, std::size_t n)
	The seqan3::dna3bs 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

The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)).

This alphabet represents a reduced version that can be used when dealing with bisulfite-converted data. All 'C's are converted to a 'T' in order to allow comparison of normal sequences with bisulfite-converted sequences. For completeness, this nucleotide alphabet has a complement table, however, it is not recommended to use it when dealing with bisulfite data because the complement of T is ambiguous in reads from bisulfite sequencing. A 'T' can represent a true thymidine or an unmethylated 'C' that was converted into a 'T'. Therefore, complementing a dna4bs sequence will further reduce the alphabet to only 'T' and 'A', thereby loosing all information about 'G'. When working with bisulfite data, we recommend to create the reverse complement of the dna4/5/15 range first and convert to dna3bs later. This avoids simplifying the data by automatically setting 'A' as the complement of 'C'. As an example: The sequence 'ACGTGC' in dna4 would be 'ATGTGT' in dna3bs. The complement of this dna3bs sequence would be 'TATATA', however when complementing the dna4 sequence first and afterwards transforming it into dna3bs, it would be 'TGTATG' which preserves more information from the original sequence.

Like most alphabets, this alphabet cannot be initialised directly from its character representation. Instead initialise/assign from the character literal or use the function seqan3::dna3bs::assign_char().

#include <seqan3/alphabet/nucleotide/dna3bs.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_dna3bs;
 
    seqan3::dna3bs my_letter{'A'_dna3bs};
 
    my_letter.assign_char('C'); // all C will be converted to T.
    if (my_letter.to_char() == 'T')
        seqan3::debug_stream << "yeah\n"; // "yeah";
 
    my_letter.assign_char('F'); // unknown characters are implicitly converted to A.
    if (my_letter.to_char() == 'A')
        seqan3::debug_stream << "yeah\n"; // "yeah";
 
    return 0;
}

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< dna3bs , 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 dna3bs seqan3::nucleotide_base< dna3bs , 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""_dna3bs() [1/2]

dna3bs_vector operator""_dna3bs	(	char const *	s,
		std::size_t	n
	)

Returns: seqan3::dna3bs_vector

You can use this string literal to easily assign to dna3bs_vector:

#include <seqan3/alphabet/nucleotide/dna3bs.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_dna3bs;
 
    seqan3::dna3bs_vector foo{"ACGTTA"_dna3bs}; // ATGTTA
    seqan3::dna3bs_vector bar = "ATGTTA"_dna3bs;
 
    if (foo == bar)
        seqan3::debug_stream << "yeah\n"; // "yeah";
 
    auto bax = "ACGTTA"_dna3bs;
 
    return 0;
}

◆ operator""_dna3bs() [2/2]

constexpr dna3bs operator""_dna3bs ( char const c )

Returns: seqan3::dna3bs

◆ 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
	)

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.

◆ complement_table

constexpr std::array< dna3bs, dna3bs::alphabet_size > seqan3::dna3bs::complement_table

staticconstexprprivate

Initial value:

{
    'T'_dna3bs,    
    'T'_dna3bs,    
    'A'_dna3bs     
}

The complement table.

◆ rank_to_char

constexpr char_type seqan3::dna3bs::rank_to_char[alphabet_size]

staticconstexprprivate

Initial value:

{
        'A',
        'G',
        'T'
    }

Value to char conversion table.

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

seqan3/alphabet/nucleotide/dna3bs.hpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Private Types

Private Attributes

Static Private Attributes

Related Functions

Detailed Description

Member Typedef Documentation

◆ char_type

◆ rank_type

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_rank()

Complexity

Exceptions

◆ char_is_valid()

Complexity

Exceptions

◆ complement()

Complexity

Exceptions

◆ to_char()

Complexity

Exceptions

◆ to_rank()

Complexity

Exceptions

Friends And Related Function Documentation

◆ operator""_dna3bs() [1/2]

◆ operator""_dna3bs() [2/2]

◆ save_minimal()

Member Data Documentation

◆ alphabet_size

◆ complement_table

◆ rank_to_char