SeqAn3
seqan3::qualified< sequence_alphabet_t, quality_alphabet_t > Class Template Reference

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 >:
[legend]

Public Types

using char_type = underlying_char_t< sequence_alphabet_type >
 Equals the char_type of sequence_alphabet_type.
 
using phred_type = underlying_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 rank_type = detail::min_viable_uint_t< size - 1 >
 The type of the alphabet when represented as a number (e.g. via to_rank()).
 
using sequence_alphabet_type = sequence_alphabet_t
 First template parameter as member type.
 

Public Member Functions

Constructors, destructor and assignment
constexpr qualified ()=default
 
constexpr qualified (qualified const &)=default
 
constexpr qualified (qualified &&)=default
 
constexpr qualifiedoperator= (qualified const &)=default
 
constexpr qualifiedoperator= (qualified &&)=default
 
 ~qualified ()=default
 
constexpr qualified (component_type const alph)
 Construction via a value of one of the components. More...
 
constexpr qualified (indirect_component_type const alph)
 Construction via a value of a subtype that is assignable to one of the components. More...
 
constexpr qualifiedoperator= (component_type const alph)
 Assignment via a value of one of the components. More...
 
constexpr qualifiedoperator= (indirect_component_type const alph)
 Assignment via a value of a subtype that is assignable to one of the components. More...
 
Write functions
constexpr qualifiedassign_char (char_type const c)
 Assign from a character. This modifies the internal sequence letter.
 
constexpr qualifiedassign_phred (phred_type const c)
 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 nucleotide_concept< 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
 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...
 
constexpr derived_type & assign_char (std::conditional_t< std::Same< char_type, void >, char, char_type > const c) noexcept
 Assign from a character. More...
 

Static Public Attributes

static detail::min_viable_uint_t< size > constexpr value_size = size
 The size of the alphabet, i.e. the number of different values it can take.
 

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 seqan3::alphabet_concept

You can expect these functions on all types that implement seqan3::alphabet_concept.

template<typename alphabet_type >
using underlying_char_t = typename underlying_char< alphabet_type >::type
 The char_type of the alphabet. [type metafunction shortcut]. More...
 
char_type to_char (alphabet_concept const alph)
 Returns the alphabet letter's value in character representation. More...
 
alphabet_concept && assign_char (alphabet_concept &&alph, char_type const chr)
 Returns the alphabet letter's value in character representation. More...
 
Requirements for seqan3::semi_alphabet_concept

You can expect these functions on all types that implement seqan3::semi_alphabet_concept.

template<typename semi_alphabet_type >
using underlying_rank_t = typename underlying_rank< semi_alphabet_type >::type
 The rank_type of the semi_alphabet. [type metafunction shortcut]. More...
 
template<typename alphabet_type >
constexpr auto alphabet_size_v = alphabet_size<alphabet_type>::value
 The size of the alphabet. [value metafunction shortcut]. More...
 
rank_type to_rank (semi_alphabet_concept const alph)
 Returns the alphabet letter's value in rank representation. More...
 
semi_alphabet_concept && assign_rank (semi_alphabet_concept &&alph, rank_type const rank)
 Returns the alphabet letter's value in rank representation. 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...
 
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...
 
Comparison operators

Free function (in-)equality comparison operators that forward to member operators (for types != self).

constexpr bool operator== (indirect_component_type const &lhs, cartesian_composition< qualified< sequence_alphabet_t, quality_alphabet_t >, component_types... > const &rhs)
 
constexpr bool operator!= (indirect_component_type const &lhs, cartesian_composition< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const &rhs)
 
constexpr bool operator< (indirect_component_type const &lhs, cartesian_composition< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const &rhs)
 
constexpr bool operator> (indirect_component_type const &lhs, cartesian_composition< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const &rhs)
 
constexpr bool operator<= (indirect_component_type const &lhs, cartesian_composition< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const &rhs)
 
constexpr bool operator>= (indirect_component_type const &lhs, cartesian_composition< qualified< sequence_alphabet_t, quality_alphabet_t >, indirect_component_types... > const &rhs)
 

Detailed Description

template<alphabet_concept sequence_alphabet_t, quality_concept quality_alphabet_t>
class seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >

Joins an arbitrary alphabet with a quality alphabet.

Template Parameters
sequence_alphabet_tType of the alphabet; must satisfy seqan3::alphabet_concept.
quality_alphabet_tType of the quality; must satisfy seqan3::quality_concept.

This composition 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 composition 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 composition, while the character values are taken from the sequence alphabet and the phred values are taken from the quality alphabet.

As with all seqan3::cartesian_composition 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::cartesian_composition itself fulfils both seqan3::alphabet_concept and seqan3::quality_concept.

Constructor & Destructor Documentation

◆ qualified() [1/2]

template<alphabet_concept sequence_alphabet_t, quality_concept quality_alphabet_t>
constexpr seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >::qualified ( component_type const  alph)
inline

Construction via a value of one of the components.

Template Parameters
component_typeMust be one uniquely contained in the type list of the composition.
Parameters
alphThe value of a component that should be assigned.

Note: Since the cartesian_composition 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<alphabet_concept sequence_alphabet_t, quality_concept quality_alphabet_t>
constexpr seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >::qualified ( indirect_component_type const  alph)
inline

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

Template Parameters
indirect_component_typeType that models the seqan3::is_assignable_concept for one of the component types.
Parameters
alphThe value that should be assigned.

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

Note: Since the cartesian_composition 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_char()

template<typename derived_type, size_t size, typename char_t = char>
constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_char ( std::conditional_t< std::Same< char_type, void >, char, char_type > const  c)
inlinenoexceptinherited

Assign from a character.

Satisfies the seqan3::alphabet_concept::assign_char() requirement via the seqan3::assign_char() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ 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.

Satisfies the seqan3::semi_alphabet_concept::assign_rank() requirement via the seqan3::assign_rank() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ complement()

template<alphabet_concept sequence_alphabet_t, quality_concept 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::nucleotide_concept::complement

◆ operator=() [1/2]

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

Assignment via a value of one of the components.

Template Parameters
component_typeOne of the component types. Must be uniquely contained in the type list of the composition.
Parameters
alphThe value of a component that should be assigned.

Note: Since the cartesian_composition 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<alphabet_concept sequence_alphabet_t, quality_concept quality_alphabet_t>
constexpr qualified& seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >::operator= ( indirect_component_type const  alph)
inline

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

Template Parameters
indirect_component_typeType that models the seqan3::is_assignable_concept for one of the component types.
Parameters
alphThe value of a component that should be assigned.

Note: Since the cartesian_composition 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).

Satisfies the seqan3::semi_alphabet_concept::to_rank() requirement via the to_rank() wrapper.

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 >>
related

Type deduction guide enables usage of qualified without specifying template args.


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