seqan3::phred_base< derived_type, size > Class Template Reference

A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets. More...

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

Inheritance diagram for seqan3::phred_base< derived_type, size >:

Public Types
Member types
using	phred_type = int8_t
	The integer representation of the quality score.

Public Member Functions
Read functions
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in Phred score representation.
Write functions
constexpr derived_type &	assign_phred (phred_type const p) noexcept
	Assign from the numeric Phred score value.
Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char >
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.
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).
constexpr derived_type &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters.
constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Private Types
using	base_t = alphabet_base< derived_type, size, char >
	The base type.

Static Private Member Functions
static constexpr rank_type	char_to_rank (char_type const chr)
	Returns the rank representation of character.
static constexpr char_type	rank_to_char (rank_type const rank)
	Returns the character representation of rank.

Private Attributes
friend	base_t
	Befriend the base type so it can access seqan3::alphabet_base::char_to_rank and seqan3::alphabet_base::rank_to_char.

Static Private Attributes
static constexpr std::array< rank_type, 256 >	phred_to_rank
	Phred to rank conversion table.
static constexpr std::array< phred_type, alphabet_size >	rank_to_phred
	Rank to phred conversion table.

Constructors, destructor and assignment
friend	derived_type
	Befriend the derived_type so it can instantiate.
constexpr	phred_base () noexcept=default
	Defaulted.
constexpr	phred_base (phred_base const &) noexcept=default
	Defaulted.
constexpr	phred_base (phred_base &&) noexcept=default
	Defaulted.
constexpr phred_base &	operator= (phred_base const &) noexcept=default
	Defaulted.
constexpr phred_base &	operator= (phred_base &&) noexcept=default
	Defaulted.
	~phred_base () noexcept=default
	Defaulted.
template<typename other_qual_type > requires (!std::same_as<phred_base, other_qual_type>) && (!std::same_as<derived_type, other_qual_type>) && quality_alphabet<other_qual_type>
constexpr	phred_base (other_qual_type const &other) noexcept
	Allow explicit construction from any other quality type by means of the Phred score representation.

Additional Inherited Members
Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char >
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.
Protected Types inherited from seqan3::alphabet_base< derived_type, size, char >
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()).

Detailed Description

template<typename derived_type, size_t size>
class seqan3::phred_base< derived_type, size >

A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets.

Template Parameters

derived_type	The CRTP parameter type.
size	The size of the alphabet.

This entity is stable. Since version 3.1.

Member Typedef Documentation

phred_type

template<typename derived_type , size_t size>

using seqan3::phred_base< derived_type, size >::phred_type = int8_t

The integer representation of the quality score.

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

phred_base()

template<typename derived_type , size_t size>

template<typename other_qual_type >
requires (!std::same_as<phred_base, other_qual_type>) && (!std::same_as<derived_type, other_qual_type>) && quality_alphabet<other_qual_type>

constexpr seqan3::phred_base< derived_type, size >::phred_base ( other_qual_type const &  other )

inlineexplicitconstexprnoexcept

Allow explicit construction from any other quality type by means of the Phred score representation.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Member Function Documentation

assign_phred()

template<typename derived_type , size_t size>

constexpr derived_type & seqan3::phred_base< derived_type, size >::assign_phred ( phred_type const  p )

inlineconstexprnoexcept

Assign from the numeric Phred score value.

Satisfies the seqan3::writable_quality_alphabet requirement via the seqan3::assign_rank_to() wrapper.

See also

quality

Complexity

Constant.

This entity is stable. Since version 3.1.

char_to_rank()

template<typename derived_type , size_t size>

static constexpr rank_type seqan3::phred_base< derived_type, size >::char_to_rank ( char_type const  chr )

inlinestaticconstexprprivate

Returns the rank representation of character.

This function is required by seqan3::alphabet_base.

rank_to_char()

template<typename derived_type , size_t size>

static constexpr char_type seqan3::phred_base< derived_type, size >::rank_to_char ( rank_type const  rank )

inlinestaticconstexprprivate

Returns the character representation of rank.

This function is required by seqan3::alphabet_base.

to_phred()

template<typename derived_type , size_t size>

constexpr phred_type seqan3::phred_base< derived_type, size >::to_phred ( ) const

inlineconstexprnoexcept

Return the alphabet's value in Phred score representation.

See also

quality

This entity is stable. Since version 3.1.

Member Data Documentation

phred_to_rank

template<typename derived_type , size_t size>

constexpr std::array<rank_type, 256> seqan3::phred_base< derived_type, size >::phred_to_rank

staticconstexprprivate

Initial value:

{
        []() constexpr {
            std::array<rank_type, 256> ret{};
 
            for (int64_t i = std::numeric_limits<phred_type>::lowest();
                 i <= std::numeric_limits<phred_type>::max();
                 ++i)
            {
                if (i < derived_type::offset_phred) 
                    ret[static_cast<rank_type>(i)] = 0;
                else if (i >= derived_type::offset_phred + alphabet_size) 
                    ret[static_cast<rank_type>(i)] = alphabet_size - 1;
                else 
                    ret[static_cast<rank_type>(i)] = i - derived_type::offset_phred;
            }
 
            return ret;
        }()
    }

Phred to rank conversion table.

rank_to_phred

template<typename derived_type , size_t size>

constexpr std::array<phred_type, alphabet_size> seqan3::phred_base< derived_type, size >::rank_to_phred

staticconstexprprivate

Initial value:

{
        []() constexpr {
            std::array<phred_type, alphabet_size> ret{};
 
            for (size_t i = 0; i < alphabet_size; ++i)
                ret[i] = i + derived_type::offset_phred;
 
            return ret;
        }()
    }

Rank to phred conversion table.

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

• phred_base.hpp