Joins an arbitrary alphabet with a quality alphabet. More...

#include <bio/alphabet/quality/qualified.hpp>

Inheritance diagram for bio::alphabet::qualified< sequence_alphabet_t, quality_alphabet_t >:

Public Types
using	char_type = char_t< sequence_alphabet_type >
	Equals the char_type of sequence_alphabet_type.

using	phred_type = phred_t< quality_alphabet_type >
	Equals the phred_type of the quality_alphabet_type.

using	quality_alphabet_type = quality_alphabet_t
	Second template parameter as member type.

using	sequence_alphabet_type = sequence_alphabet_t
	First template parameter as member type.

Public Member Functions
Constructors, destructor and assignment
constexpr	qualified () noexcept=default
	Defaulted.

constexpr	qualified (qualified const &) noexcept=default
	Defaulted.

constexpr	qualified (qualified &&) noexcept=default
	Defaulted.

constexpr qualified &	operator= (qualified const &) noexcept=default
	Defaulted.

constexpr qualified &	operator= (qualified &&) noexcept=default
	Defaulted.

	~qualified () noexcept=default
	Defaulted.

constexpr	qualified (component_type const alph) noexcept
	Construction via a value of one of the components.

constexpr	qualified (indirect_component_type const alph) noexcept
	Construction via a value of a subtype that is assignable to one of the components.

constexpr qualified &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components.

constexpr qualified &	operator= (indirect_component_type const alph) noexcept
	Assignment via a value of a subtype that is assignable to one of the components.

Write functions
constexpr qualified &	assign_char (char_type const c) noexcept
	Assign from a character. This modifies the internal sequence letter.

constexpr qualified &	assign_phred (phred_type const c) noexcept
	Assign from a phred value. This modifies the internal quality letter.

Read functions
constexpr phred_type	to_phred () const noexcept
	Return the phred value. This reads the internal quality letter.

constexpr char_type	to_char () const noexcept
	Return a character. This reads the internal sequence letter.

constexpr qualified	complement () const noexcept
	Return a qualified where the quality is preserved, but the sequence letter is complemented.

Read functions
All read operations are constant complexity.
constexpr	operator type () const noexcept
	Implicit cast to a single letter. Works only if the type is unique in the type list.

Read functions
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).

Write functions
constexpr derived_type &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters.

constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Static Public Member Functions
static constexpr bool	char_is_valid (char_type const c) noexcept
	Validate whether a character is valid in the sequence alphabet.

Static Public Attributes
static constexpr size_t	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take.

Protected Types
Member types
using	rank_type = meta::detail::min_viable_uint_t< size - 1 >
	The type of the alphabet when represented as a number (e.g. via to_rank()).

Related Functions
(Note that these are not member functions.)
template<typename sequence_alphabet_type , typename quality_alphabet_type >
	qualified (sequence_alphabet_type &&, quality_alphabet_type &&) -> qualified< std::decay_t< sequence_alphabet_type >, std::decay_t< quality_alphabet_type > >
	Type deduction guide enables usage of qualified without specifying template args.

Detailed Description

template<writable_alphabet sequence_alphabet_t, writable_quality quality_alphabet_t>
class bio::alphabet::qualified< sequence_alphabet_t, quality_alphabet_t >

Joins an arbitrary alphabet with a quality alphabet.

Template Parameters

sequence_alphabet_t	Type of the alphabet; must satisfy bio::alphabet::writable_alphabet.
quality_alphabet_t	Type of the quality; must satisfy bio::alphabet::writable_quality.

This composite pairs an arbitrary alphabet with a quality alphabet, where each alphabet character is stored together with its quality score in a single value. That way, you can can conveniently access the character and score information at each position of the qualified-sequence. The use case that this was designed for is a nucleotide sequence with corresponding quality scores, e.g. obtained when reading in a FASTQ file of Illumina reads. The composite also allows to store quality scores for different or extended alphabets like a qualified<char, phred42> or a qualified<gapped<dna4>, phred42> sequence. The rank values correspond to numeric values in the size of the composite, while the character values are taken from the sequence alphabet and the phred values are taken from the quality alphabet.

As with all bio::alphabet::tuple_base s you may access the individual alphabet letters in regular c++ tuple notation, i.e. get<0>(t) and objects can be brace-initialised with the individual members.

#include <bio/alphabet/quality/qualified.hpp>
#include <bio/alphabet/quality/phred42.hpp>
#include <bio/alphabet/nucleotide/dna4.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::qualified<bio::alphabet::dna4, bio::alphabet::phred42> letter{'A'_dna4, bio::alphabet::phred42{7}};
    fmt::print("{} {} {}\n",
               bio::alphabet::to_rank(letter),
               bio::alphabet::to_rank(get<0>(letter)),
               bio::alphabet::to_rank(get<1>(letter)));
    // 28 0 7
 
    fmt::print("{} {} {}\n",
               bio::alphabet::to_char(letter),
               bio::alphabet::to_char(get<0>(letter)),
               bio::alphabet::to_char(get<1>(letter)));
    // A A (
 
    fmt::print("{} {}\n", bio::alphabet::to_phred(letter), bio::alphabet::to_phred(get<1>(letter)));
    // 7 7
 
    // modify via structured bindings and references:
    auto & [ seq_l, qual_l ] = letter;
    seq_l = 'G'_dna4;
    fmt::print("{}\n", bio::alphabet::to_char(letter));
    // G
}

This bio::alphabet::tuple_base itself fulfils both bio::alphabet::writable_alphabet and bio::alphabet::writable_quality.

Constructor & Destructor Documentation

◆ qualified() [1/2]

template<writable_alphabet sequence_alphabet_t, writable_quality quality_alphabet_t>

constexpr bio::alphabet::qualified< sequence_alphabet_t, quality_alphabet_t >::qualified ( component_type const alph )

inlineconstexprnoexcept

Construction via a value of one of the components.

Template Parameters

component_type Must be one uniquely contained in the type list of the composite.

Parameters

alph	The value of a component that should be assigned.

Note: Since the tuple_base is a CRTP base class, we show the working examples with one of its derived classes (bio::alphabet::qualified).

#include <bio/alphabet/nucleotide/dna4.hpp>
#include <bio/alphabet/quality/phred42.hpp>
#include <bio/alphabet/quality/qualified.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::qualified<bio::alphabet::dna4, bio::alphabet::phred42> letter1{'C'_dna4};
    // creates {'C'_dna4, bio::alphabet::phred42{0}}
    bio::alphabet::qualified<bio::alphabet::dna4, bio::alphabet::phred42> letter2{bio::alphabet::phred42{1}};
    // creates {'A'_dna4, bio::alphabet::phred42{1}}
 
    if (letter1 == letter2)
        fmt::print("{}", "yeah\n"); // yeah
}

◆ qualified() [2/2]

template<writable_alphabet sequence_alphabet_t, writable_quality quality_alphabet_t>

constexpr bio::alphabet::qualified< sequence_alphabet_t, quality_alphabet_t >::qualified ( indirect_component_type const alph )

inlineconstexprnoexcept

Construction via a value of a subtype that is assignable to one of the components.

Template Parameters

indirect_component_type Type that models bio::alphabet::weakly_assignable_from for one of the component types.

Parameters

alph	The value that should be assigned.

Note that the value will be assigned to the FIRST type T that fulfils assignable_from<T, indirect_component_type>, regardless if other types are also fit for assignment.

Note: Since the tuple_base is a CRTP base class, we show the working examples with one of its derived classes (bio::alphabet::qualified).

#include <bio/alphabet/nucleotide/all.hpp>
#include <bio/alphabet/quality/phred42.hpp>
#include <bio/alphabet/quality/qualified.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
    using namespace bio::alphabet::literals;
 
    // The following creates {'C'_dna4, phred42{0}}
    bio::alphabet::qualified<bio::alphabet::dna4, bio::alphabet::phred42> letter1{'C'_dna4};
    // The following also creates {'C'_dna4, bio::alphabet::phred42{0}}, since rna4 assignable to dna4
    bio::alphabet::qualified<bio::alphabet::dna4, bio::alphabet::phred42> letter2{'C'_rna4};
 
    if (letter1 == letter2)
        fmt::print("{}", "yeah\n"); // yeah
}

Member Function Documentation

◆ assign_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type & bio::alphabet::base< derived_type, size, char_t >::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 bio::alphabet::assign_char_to, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type & bio::alphabet::base< derived_type, size, char_t >::assign_rank ( rank_type const c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ complement()

template<writable_alphabet sequence_alphabet_t, writable_quality quality_alphabet_t>

constexpr qualified bio::alphabet::qualified< sequence_alphabet_t, quality_alphabet_t >::complement ( ) const

inlineconstexprnoexcept

Return a qualified where the quality is preserved, but the sequence letter is complemented.

See also: bio::alphabet::complement; bio::alphabet::nucleotide::complement

◆ operator type()

constexpr bio::alphabet::tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t > , component_types >::operator type ( ) const

inlineconstexprnoexceptinherited

Implicit cast to a single letter. Works only if the type is unique in the type list.

◆ operator=() [1/2]

template<writable_alphabet sequence_alphabet_t, writable_quality quality_alphabet_t>

constexpr qualified & bio::alphabet::qualified< sequence_alphabet_t, quality_alphabet_t >::operator= ( component_type const alph )

inlineconstexprnoexcept

Assignment via a value of one of the components.

Template Parameters

component_type One of the component types. Must be uniquely contained in the type list of the composite.

Parameters

alph	The value of a component that should be assigned.

Note: Since the tuple_base is a CRTP base class, we show the working examples with one of its derived classes (bio::alphabet::qualified).

#include <bio/alphabet/nucleotide/dna4.hpp>
#include <bio/alphabet/quality/phred42.hpp>
#include <bio/alphabet/quality/qualified.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::qualified<bio::alphabet::dna4, bio::alphabet::phred42> letter1{'T'_dna4, bio::alphabet::phred42{1}};
 
    letter1 = 'C'_dna4;           // yields {'C'_dna4, bio::alphabet::phred42{1}}
    letter1 = bio::alphabet::phred42{2}; // yields {'C'_dna4, bio::alphabet::phred42{2}}
}

◆ operator=() [2/2]

template<writable_alphabet sequence_alphabet_t, writable_quality quality_alphabet_t>

constexpr qualified & bio::alphabet::qualified< sequence_alphabet_t, quality_alphabet_t >::operator= ( indirect_component_type const alph )

inlineconstexprnoexcept

Assignment via a value of a subtype that is assignable to one of the components.

Template Parameters

indirect_component_type Type that models bio::alphabet::weakly_assignable_from for one of the component types.

Parameters

alph	The value of a component that should be assigned.

Note: Since the tuple_base is a CRTP base class, we show the working examples with one of its derived classes (bio::alphabet::qualified).

#include <bio/alphabet/nucleotide/all.hpp>
#include <bio/alphabet/quality/phred42.hpp>
#include <bio/alphabet/quality/qualified.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
    using namespace bio::alphabet::literals;
 
    bio::alphabet::qualified<bio::alphabet::dna4, bio::alphabet::phred42> letter1{'T'_dna4, bio::alphabet::phred42{1}};
 
    letter1 = 'C'_rna4; // yields {'C'_dna4, bio::alphabet::phred42{1}}
}

◆ to_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr rank_type bio::alphabet::base< derived_type, size, char_t >::to_rank ( ) const

inlineconstexprnoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for bio::alphabet::to_rank, required to model bio::alphabet::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

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

bio/alphabet/quality/qualified.hpp

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Related Functions

Detailed Description

Constructor & Destructor Documentation

◆ qualified() [1/2]

◆ qualified() [2/2]

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_rank()

Complexity

Exceptions

◆ complement()

◆ operator type()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ to_rank()

Complexity

Exceptions