seqan3::phred68legacy Class Reference

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

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

Inheritance diagram for seqan3::phred68legacy:

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.
Public Member Functions inherited from seqan3::quality_base< phred68legacy, 68 >
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in Phred score representation. More...
constexpr phred68legacy &	assign_phred (phred_type const p) noexcept
	Assign from the numeric Phred score value. More...
constexpr	quality_base (other_qual_type const &other) noexcept
	Allow explicit construction from any other quality type by means of the Phred score representation. 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...

Static Public Attributes
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.
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...

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

Private Attributes
friend	base_t
	Befriend seqan3::quality_base.

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...
Related Functions inherited from semialphabet
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...

Additional Inherited Members
Public Types inherited from seqan3::quality_base< phred68legacy, 68 >
using	phred_type = int8_t
	The integer representation of the quality score. 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

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
}

Friends And Related Function Documentation

operator""_phred68legacy() [1/2]

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

related

The seqan3::phred68legacy string literal.

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 )

related

The seqan3::phred68legacy char literal.

Returns

seqan3::phred68legacy

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

• seqan3/alphabet/quality/phred68legacy.hpp