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

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

Inheritance diagram for seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >:

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

using	phred_type = alphabet_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. More...

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

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

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

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

qualified &	assign_char_strictly (char_type const c)
	Strict 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 requires NucleotideAlphabet< sequence_alphabet_t >
	Return a qualified where the quality is preserved, but the sequence letter is complemented. More...

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.

Comparison operators (against indirect component_list)
`*this` is cast to the component type before comparison. (These overloads enable comparison for all types that a component type is comparable with).
constexpr bool	operator== (indirect_component_type const rhs) const noexcept

constexpr bool	operator!= (indirect_component_type const rhs) const noexcept

constexpr bool	operator< (indirect_component_type const rhs) const noexcept

constexpr bool	operator> (indirect_component_type const rhs) const noexcept

constexpr bool	operator<= (indirect_component_type const rhs) const noexcept

constexpr bool	operator>= (indirect_component_type const rhs) const noexcept

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

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

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 detail::min_viable_uint_t< size > constexpr	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 = 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. More...

Requirements for std::Swappable
You can expect these functions on all types that implement std::Swappable.
void	swap (t &lhs, t &rhs)
	Swaps the contents of two objects. More...

Requirements for std::EqualityComparable
You can expect these functions on all types that implement std::Equality_comparable.
bool	operator== (type const &lhs, type const &rhs)
	(In-)Equality comparison. More...

bool	operator!= (type const &lhs, type const &rhs)
	(In-)Equality comparison. More...

Comparison operators
Free function (in-)equality comparison operators that forward to member operators (for types != self).
constexpr bool	operator== (indirect_component_type const lhs, alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, component_types... > const rhs) noexcept

constexpr bool	operator!= (indirect_component_type const lhs, alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator< (indirect_component_type const lhs, alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator> (indirect_component_type const lhs, alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator<= (indirect_component_type const lhs, alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator>= (indirect_component_type const lhs, alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const rhs) noexcept

Requirements for std::StrictTotallyOrdered
You can expect these functions on all types that implement std::StrictTotallyOrdered.
bool	operator< (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator> (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator<= (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator>= (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

Detailed Description

template<WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet quality_alphabet_t>
class seqan3::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 seqan3::WritableAlphabet.
quality_alphabet_t	Type of the quality; must satisfy seqan3::WritableQualityAlphabet.

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 seqan3::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.

qualified<dna4, phred42> letter{'A'_dna4, phred42{7}};
debug_stream << int(to_rank(letter)) << ' '
          << int(to_rank(get<0>(letter))) << ' '
          << int(to_rank(get<1>(letter))) << '\n';
// 28 0 7
debug_stream << to_char(letter) << ' '
          << to_char(get<0>(letter)) << ' '
          << to_char(get<1>(letter)) << '\n';
// A A (
debug_stream << int(to_phred(letter)) << ' '
//        << int(to_phred(get<0>(letter))) << ' ' // dna4 doesn't have a phred
          << int(to_phred(get<1>(letter))) << '\n';
// 7 7
// modify via structured bindings and references:
auto & [ seq_l, qual_l ] = letter;
seq_l = 'G'_dna4;
debug_stream << to_char(letter) << '\n';
// G

This seqan3::alphabet_tuple_base itself fulfils both seqan3::WritableAlphabet and seqan3::WritableQualityAlphabet.

Constructor & Destructor Documentation

◆ qualified() [1/2]

template<WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet quality_alphabet_t>

constexpr seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >::qualified ( component_type const alph )

inlinenoexcept

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 alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

qualified<dna4, phred42> letter1{'C'_dna4}; // creates {'C'_dna4, phred42{0}}

qualified<dna4, phred42> letter2{phred42{1}}; // creates {'A'_dna4, phred42{1}}

◆ qualified() [2/2]

template<WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet quality_alphabet_t>

constexpr seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >::qualified ( indirect_component_type const alph )

inlinenoexcept

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

Template Parameters

indirect_component_type Type that models seqan3::WeaklyAssignable 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<T, indirect_component_type>, regardless if other types are also fit for assignment.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

// The following creates {'C'_dna4, phre42{0}}
qualified<dna4, phred42> letter1{'C'_dna4};
// The following also creates {'C'_dna4, phred42{0}}, since rna4 assignable to dna4
qualified<dna4, phred42> letter2{'C'_rna4};
if (letter1 == letter2)
    debug_stream << "yeah\n"; // yeah

Member Function Documentation

◆ assign_rank()

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

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_rank ( rank_type const c )

inlinenoexceptinherited

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.

◆ complement()

template<WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet quality_alphabet_t>

constexpr qualified seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >::complement ( ) const

inlinenoexcept

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

See also: seqan3::complement; seqan3::NucleotideAlphabet::complement

◆ operator=() [1/2]

template<WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet quality_alphabet_t>

constexpr qualified& seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >::operator= ( component_type const alph )

inlinenoexcept

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 alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

qualified<dna4, phred42> letter1{'T'_dna4, phred42{1}};
letter1 = 'C'_dna4; // yields {'C'_dna4, phred42{1}}
letter1 = phred42{2}; // yields {'C'_dna4, phred42{2}}

◆ operator=() [2/2]

template<WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet quality_alphabet_t>

constexpr qualified& seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >::operator= ( indirect_component_type const alph )

inlinenoexcept

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

Template Parameters

indirect_component_type Type that models seqan3::WeaklyAssignable for one of the component types.

Parameters

alph	The value of a component that should be assigned.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

qualified<dna4, phred42> letter1{'T'_dna4, phred42{1}};
letter1 = 'C'_rna4; // yields {'C'_dna4, phred42{1}}

◆ to_rank()

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

constexpr rank_type seqan3::alphabet_base< derived_type, size, char_t >::to_rank ( ) const

inlinenoexceptinherited

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.

Friends And Related Function Documentation

◆ qualified()

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 >>

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

seqan3/alphabet/quality/qualified.hpp

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Related Functions

Detailed Description

template<WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet quality_alphabet_t> class seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >

Constructor & Destructor Documentation

◆ qualified() [1/2]

◆ qualified() [2/2]

Member Function Documentation

◆ assign_rank()

Complexity

Exceptions

◆ complement()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ to_rank()

Complexity

Exceptions

Friends And Related Function Documentation

◆ qualified()

template<WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet quality_alphabet_t>
class seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >