SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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 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...
 
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...
 
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...
 
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()).
 
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()).
 
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()).
 
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_sizerank_to_char
 Rank to char conversion table. More...
 
static constexpr std::array< phred_type, alphabet_sizerank_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_typeThe CRTP parameter type.
sizeThe 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
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()

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
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< 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
{
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
{
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
{
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
{
for (size_t i = 0; i < alphabet_size; ++i)
ret[i] = i + derived_type::offset_phred;
return ret;
}()
}

Rank to phred conversion table.


The documentation for this class was generated from the following file:
seqan3::alphabet_base< derived_type, size, char >::alphabet_size
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.
Definition: alphabet_base.hpp:176
seqan3::alphabet_base< derived_type, size, char >::rank_type
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition: alphabet_base.hpp:64
std::array< rank_type, 256 >
std::numeric_limits