Joins an arbitrary alphabet with a quality alphabet. More...
#include <seqan3/alphabet/quality/qualified.hpp>
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) | |
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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... | |
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... | |
Joins an arbitrary alphabet with a quality alphabet.
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.
This seqan3::alphabet_tuple_base itself fulfils both seqan3::WritableAlphabet and seqan3::WritableQualityAlphabet.
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inlinenoexcept |
Construction via a value of one of the components.
component_type | Must be one uniquely contained in the type list of the composite. |
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).
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inlinenoexcept |
Construction via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models seqan3::WeaklyAssignable 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 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).
|
inlinenoexceptinherited |
Assign from a numeric value.
c | The rank to be assigned. |
Provides an implementation for seqan3::assign_rank_to, required to model seqan3::Semialphabet.
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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inlinenoexcept |
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 composite. |
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).
|
inlinenoexcept |
Assignment via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models seqan3::WeaklyAssignable for one of the component types. |
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).
|
inlinenoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Provides an implementation for seqan3::to_rank, required to model seqan3::Semialphabet.
Constant.
Guaranteed not to throw.
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related |
Type deduction guide enables usage of qualified without specifying template args.