Joins an arbitrary alphabet with a quality alphabet. More...
#include <seqan3/alphabet/quality/qualified.hpp>
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 qualified & | operator= (qualified const &)=default |
constexpr qualified & | operator= (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 qualified & | operator= (component_type const alph) |
Assignment via a value of one of the components. More... | |
constexpr qualified & | operator= (indirect_component_type const alph) |
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) |
Assign from a character. This modifies the internal sequence letter. | |
constexpr qualified & | assign_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) | |
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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) |
Joins an arbitrary alphabet with a quality alphabet.
sequence_alphabet_t | Type of the alphabet; must satisfy seqan3::alphabet_concept. |
quality_alphabet_t | Type 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.
This seqan3::cartesian_composition itself fulfils both seqan3::alphabet_concept and seqan3::quality_concept.
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inline |
Construction via a value of one of the components.
component_type | Must be one uniquely contained in the type list of the composition. |
alph | The 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).
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inline |
Construction via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models the seqan3::is_assignable_concept for one of the component types. |
alph | The 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).
|
inlinenoexceptinherited |
Assign from a character.
Satisfies the seqan3::alphabet_concept::assign_char() requirement via the seqan3::assign_char() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexceptinherited |
Assign from a numeric value.
Satisfies the seqan3::semi_alphabet_concept::assign_rank() requirement via the seqan3::assign_rank() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexcept |
Return a qualified where the quality is preserved, but the sequence letter is complemented.
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inline |
Assignment via a value of one of the components.
component_type | One of the component types. Must be uniquely contained in the type list of the composition. |
alph | The 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).
|
inline |
Assignment via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models the seqan3::is_assignable_concept for one of the component types. |
alph | The 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).
|
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.
Constant.
Guaranteed not to throw.
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related |
Type deduction guide enables usage of qualified without specifying template args.