seqan3::quality_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/quality_base.hpp>

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

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

Public Member Functions
Read functions
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in phred representation.
Write functions
constexpr derived_type &	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 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
	The size of the alphabet, i.e. the number of different values it can take.

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

Constructors, destructor and assignment
template<typename other_qual_type >
constexpr	quality_base (other_qual_type const &other) noexcept
	Allow explicit construction from any other quality type by means of the phred representation.

Detailed Description

template<typename derived_type, auto size>
class seqan3::quality_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.

Member Function Documentation

assign_char()

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char >::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.

assign_phred()

template<typename derived_type, auto size>

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

inlineconstexprnoexcept

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 derived_type& seqan3::alphabet_base< derived_type, size, char >::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.

to_char()

constexpr char_type seqan3::alphabet_base< derived_type, size, char >::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.

to_rank()

constexpr rank_type seqan3::alphabet_base< derived_type, size, char >::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.

Member Data Documentation

char_to_rank

template<typename derived_type, auto size>

constexpr std::array<rank_type, 256> seqan3::quality_base< derived_type, size >::char_to_rank

staticconstexprprotected

Initial value:

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

Char to rank conversion table.

phred_to_rank

template<typename derived_type, auto size>

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

staticconstexprprotected

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_char

template<typename derived_type, auto size>

constexpr std::array<char_type, alphabet_size> seqan3::quality_base< derived_type, size >::rank_to_char

staticconstexprprotected

Initial value:

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

Rank to char conversion table.

rank_to_phred

template<typename derived_type, auto size>

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

staticconstexprprotected

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:

• seqan3/alphabet/quality/quality_base.hpp