SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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 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.
 
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()).
 
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 phred68legacyoperator= (phred68legacy const &) noexcept=default
 Defaulted.
 
constexpr phred68legacyoperator= (phred68legacy &&) noexcept=default
 Defaulted.
 
 ~phred68legacy () noexcept=default
 Defaulted.
 
constexpr phred68legacy (phred_type const p)
 Construct from phred value.
 
Read functions
constexpr phred_type to_phred () const noexcept
 Return the alphabet's value in phred representation.
 
Write functions
constexpr phred68legacyassign_phred (phred_type const p) noexcept
 Assign from the numeric phred 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 phred68legacyassign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr phred68legacyassign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 

Static Public Attributes

static detail::min_viable_uint_t< size > constexpr alphabet_size
 The size of the alphabet, i.e. the number of different values it can take.
 
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 Protected Attributes

static std::array< rank_type, 256 > constexpr char_to_rank
 Char to rank conversion table.
 
static std::array< rank_type, 256 > constexpr phred_to_rank
 Phred to rank conversion table.
 
static std::array< char_type, alphabet_size > constexpr rank_to_char
 Rank to char conversion table.
 
static std::array< phred_type, alphabet_size > constexpr rank_to_phred
 Rank to phred conversion table.
 

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< phred68legacyoperator""_phred68legacy (char const *s, std::size_t n)
 The seqan3::phred68legacy string literal. More...
 
Requirements for std::totally_ordered

You can expect these functions on all types that implement std::totally_ordered.

bool operator< (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator<= (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator> (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator>= (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
Requirements for std::equality_comparable

You can expect these functions on all types that implement std::Equality_comparable.

bool operator== (type const &lhs, type const &rhs)
 (In-)Equality comparison. More...
 
bool operator!= (type const &lhs, type const &rhs)
 (In-)Equality comparison. More...
 
Requirements for std::swappable

You can expect these functions on all types that implement std::swappable.

void swap (t &lhs, t &rhs)
 Swaps the contents of two objects. 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.

int main()
{
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 Function Documentation

◆ assign_char()

constexpr phred68legacy & seqan3::alphabet_base< phred68legacy , size, char >::assign_char ( char_type const  c)
inlinenoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters
cThe character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_phred()

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

Assign from the numeric phred value.

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

Complexity

Constant.

◆ assign_rank()

constexpr phred68legacy & seqan3::alphabet_base< phred68legacy , size, char >::assign_rank ( rank_type const  c)
inlinenoexceptinherited

Assign from a numeric value.

Parameters
cThe rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

constexpr char_type seqan3::alphabet_base< phred68legacy , size, char >::to_char ( ) const
inlinenoexceptinherited

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.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< phred68legacy , size, char >::to_rank ( ) const
inlinenoexceptinherited

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.

Friends And Related Function Documentation

◆ operator""_phred68legacy() [1/2]

constexpr phred68legacy operator""_phred68legacy ( char const  c)
related

The seqan3::phred68legacy char literal.

Returns
seqan3::phred68legacy

◆ operator""_phred68legacy() [2/2]

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

The seqan3::phred68legacy string literal.

Parameters
[in]sA pointer to the character sequence to assign from.
[in]nThe 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>:

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) << std::endl; // prints 1 (true)
}

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