Quality type for Solexa and deprecated Illumina formats. More...

#include <seqan3/alphabet/quality/phred68legacy.hpp>

Inheritance diagram for seqan3::phred68legacy:

Public Types
Member types
using	phred_type = int8_t
	The integer representation of a quality score assignable with =operator.

Public Member Functions
Constructors, destructor and assignment
constexpr	phred68legacy () noexcept=default
	Defaulted.

constexpr	phred68legacy (phred68legacy const &) noexcept=default
	Defaulted.

constexpr	phred68legacy (phred68legacy &&) noexcept=default
	Defaulted.

constexpr phred68legacy &	operator= (phred68legacy const &) noexcept=default
	Defaulted.

constexpr phred68legacy &	operator= (phred68legacy &&) noexcept=default
	Defaulted.

	~phred68legacy () noexcept=default
	Defaulted.

constexpr	phred68legacy (phred_type const p)
	Construct from Phred score value.

Read functions
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in Phred score representation. More...

Write functions
constexpr phred68legacy &	assign_phred (phred_type const p) noexcept
	Assign from the numeric Phred score value. 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 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...

Member variables.
static constexpr phred_type	offset_phred {-5}
	The projection offset between Phred and rank score representation.

static constexpr char_type	offset_char {';'}
	The projection offset between char and rank score representation.

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...

Static Protected Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank
	Char to rank conversion table.

static constexpr std::array< rank_type, 256 >	phred_to_rank
	Phred to rank conversion table.

static constexpr std::array< char_type, alphabet_size >	rank_to_char
	Rank to char conversion table.

static constexpr std::array< phred_type, alphabet_size >	rank_to_phred
	Rank to phred conversion table.

Private Types
using	base_t = quality_base< phred68legacy, 68 >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::quality_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.

Related Functions
(Note that these are not member functions.)
Literals
constexpr phred68legacy	operator""_phred68legacy (char const c) noexcept
	The seqan3::phred68legacy char literal. More...

std::vector< phred68legacy >	operator""_phred68legacy (char const *s, std::size_t n)
	The seqan3::phred68legacy 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

Quality type for Solexa and deprecated Illumina formats.

The phred68legacy quality alphabet represents the -5-based Phred score range [-5..62] mapped to the ASCII range [';' .. '~']. It represents the Solexa and the Illumina [1.0;1.8[ standard.

#include <seqan3/alphabet/quality/phred68legacy.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    seqan3::phred68legacy phred;
    phred.assign_phred(-2);
    seqan3::debug_stream << (int) phred.to_phred() << "\n"; // -2
    seqan3::debug_stream << phred.to_char() << "\n";        // '>'
    seqan3::debug_stream << (int) phred.to_rank() << "\n";  // 3
}

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_phred()

constexpr phred68legacy & seqan3::quality_base< phred68legacy , size >::assign_phred ( phred_type const p )

inlineconstexprnoexceptinherited

Assign from the numeric Phred score value.

Satisfies the seqan3::writable_quality_alphabet::assign_phred() requirement via the seqan3::assign_rank() wrapper.

See also: Quality

Complexity

Constant.

◆ 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.

◆ 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_phred()

constexpr phred_type seqan3::quality_base< phred68legacy , size >::to_phred ( ) const

inlineconstexprnoexceptinherited

Return the alphabet's value in Phred score representation.

See also: Quality

◆ 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""_phred68legacy() [1/2]

std::vector< phred68legacy > operator""_phred68legacy	(	char const *	s,
		std::size_t	n
	)

Parameters

[in]	s	A pointer to the character sequence to assign from.
[in]	n	The length of the character sequence to assign from.

Returns: seqan3::std::vector<seqan3::phred68legacy>

You can use this string literal to easily assign to std::vector<seqan3::phred68legacy>:

#include <seqan3/alphabet/quality/phred68legacy.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/std/algorithm>
 
int main()
{
    using seqan3::operator""_phred68legacy;
 
    // directly assign to a std::vector<phred68legacy> using a string literal
    std::vector<seqan3::phred68legacy> qual_vec = "###!"_phred68legacy;
 
    // This is the same as a sequence of char literals:
    std::vector<seqan3::phred68legacy> qual_vec2 = {'#'_phred68legacy, '#'_phred68legacy,
                                                    '#'_phred68legacy, '!'_phred68legacy};
 
    seqan3::debug_stream << std::ranges::equal(qual_vec, qual_vec2) << '\n'; // prints 1 (true)
}

◆ operator""_phred68legacy() [2/2]

constexpr phred68legacy operator""_phred68legacy ( char const c )

Returns: seqan3::phred68legacy

◆ 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.

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

seqan3/alphabet/quality/phred68legacy.hpp

Public Types

Public Member Functions

Static Public Attributes

Protected Types

Static Protected Attributes

Private Types

Private Attributes

Related Functions

Detailed Description

Member Typedef Documentation

◆ char_type

◆ rank_type

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_phred()

Complexity

◆ assign_rank()

Complexity

Exceptions

◆ to_char()

Complexity

Exceptions

◆ to_phred()

◆ to_rank()

Complexity

Exceptions

Friends And Related Function Documentation

◆ operator""_phred68legacy() [1/2]

◆ operator""_phred68legacy() [2/2]

◆ save_minimal()

Member Data Documentation

◆ alphabet_size