Quality type for Solexa and deprecated Illumina formats. More...
#include <seqan3/alphabet/quality/phred68legacy.hpp>
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 value. | |
Read functions | |
constexpr phred_type | to_phred () const noexcept |
Return the alphabet's value in phred representation. | |
Write functions | |
constexpr phred68legacy & | assign_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 phred68legacy & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr phred68legacy & | 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 |
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. | |
Protected Types | |
Member types | |
using | char_type = std::conditional_t< std::same_as< char, void >, char, char > |
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()). | |
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. | |
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... | |
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.
|
inlineconstexprnoexceptinherited |
Assign from a character, implicitly converts invalid characters.
c | The character to be assigned. |
Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
|
inlineconstexprnoexceptinherited |
Assign from the numeric phred value.
Satisfies the seqan3::writable_quality_alphabet::assign_phred() requirement via the seqan3::assign_rank() wrapper.
Constant.
|
inlineconstexprnoexceptinherited |
Assign from a numeric value.
c | The rank to be assigned. |
Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
|
inlineconstexprnoexceptinherited |
Return the letter as a character of char_type.
Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
|
inlineconstexprnoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
|
related |
The seqan3::phred68legacy string literal.
[in] | s | A pointer to the character sequence to assign from. |
[in] | n | The length of the character sequence to assign from. |
You can use this string literal to easily assign to std::vector<seqan3::phred68legacy>:
|
related |
The seqan3::phred68legacy char literal.