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. | |
constexpr qualified & | assign_phred (phred_type const c) noexcept |
Assign from a Phred score value. This modifies the internal quality letter. | |
Read functions | |
constexpr phred_type | to_phred () const noexcept |
Return the Phred score 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_alphabet< 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. | |
Read functions | |
constexpr rank_type | to_rank () const noexcept |
Return the letter's numeric value (rank in the alphabet). More... | |
Write functions | |
constexpr qualified< sequence_alphabet_t, quality_alphabet_t > & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr qualified< sequence_alphabet_t, quality_alphabet_t > & | 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 constexpr detail::min_viable_uint_t< size > | alphabet_size |
The size of the alphabet, i.e. the number of different values it can take. More... | |
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()). More... | |
Private Types | |
using | base_t = alphabet_base< qualified< sequence_alphabet_t, quality_alphabet_t >,(1 *... *alphabet_size< component_types >), void > |
The base type of this class. | |
using | base_type = alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, sequence_alphabet_t, quality_alphabet_t > |
The base type. | |
using | component_list = meta::list< component_types... > |
A meta::list The types of each component in the composite. | |
using | seqan3_recursive_required_types = meta::concat< component_list, detail::transformation_trait_or_t< detail::recursive_required_types< component_types >, meta::list<> >... > |
Export this type's components and possibly the components' components in a visible manner. | |
using | seqan3_required_types = component_list |
Export this type's components in a visible manner. | |
Private Member Functions | |
constexpr void | assign_component_rank (ptrdiff_t const r) noexcept |
Assign via the rank of i-th component (does not update other components' state). | |
constexpr rank_type | to_component_rank () const noexcept |
Return the rank of the i-th component. | |
Static Private Member Functions | |
static constexpr rank_type | rank_sum_helper (component_types ... components, std::index_sequence< idx... > const &) noexcept |
For the given components, compute the combined rank. | |
Private Attributes | |
friend | derived_type |
Befriend the derived type so that it can instantiate. More... | |
rank_type | rank |
The value of the alphabet letter is stored as the rank. | |
Static Private Attributes | |
static constexpr std::array< rank_type, component_list::size()> | cummulative_alph_sizes |
The cumulative alphabet size products are cached. | |
static constexpr bool | is_component |
Is set to true if the type is contained in the type list. | |
static constexpr bool | is_unique_component |
Is set to true if the type is uniquely contained in the type list. | |
static constexpr std::array< char_type, alphabet_size > | rank_to_char |
Rank to char conversion table. More... | |
static constexpr std::array< char_type, alphabet_size > | rank_to_phred |
Rank to Phred conversion table. More... | |
static constexpr bool | seqan3_alphabet_tuple_like |
Make specialisations of this template identifiable in metapgrogramming contexts. | |
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. | |
Generic serialisation functions for all seqan3::semialphabet | |
All types that satisfy seqan3::semialphabet can be serialised via Cereal. | |
template<cereal_output_archive archive_t, semialphabet alphabet_t> | |
alphabet_rank_t< alphabet_t > | save_minimal (archive_t const &, alphabet_t const &l) |
Save an alphabet letter to stream. More... | |
Joins an arbitrary alphabet with a quality alphabet.
sequence_alphabet_t | Type of the alphabet; must satisfy seqan3::writable_alphabet. |
quality_alphabet_t | Type of the quality; must satisfy seqan3::writable_quality_alphabet. |
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 score 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::writable_alphabet and seqan3::writable_quality_alphabet.
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protectedinherited |
The type of the alphabet when represented as a number (e.g. via to_rank()).
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inlineconstexprnoexcept |
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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inlineconstexprnoexcept |
Construction via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models seqan3::weakly_assignable_from 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_from<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).
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inlineconstexprnoexceptinherited |
Assign from a character, implicitly converts invalid characters.
c | The character to be assigned. |
Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
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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inlineconstexprnoexcept |
Return a qualified where the quality is preserved, but the sequence letter is complemented.
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inlineconstexprnoexcept |
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).
|
inlineconstexprnoexcept |
Assignment via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models seqan3::weakly_assignable_from 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).
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inlineconstexprnoexceptinherited |
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 |
Save an alphabet letter to stream.
archive_t | Must satisfy seqan3::cereal_output_archive. |
alphabet_t | Type of l; must satisfy seqan3::semialphabet. |
l | The alphabet letter. |
Delegates to seqan3::to_rank.
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staticconstexprinherited |
The size of the alphabet, i.e. the number of different values it can take.
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privateinherited |
Befriend the derived type so that it can instantiate.
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staticconstexprprivate |
Rank to char conversion table.
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staticconstexprprivate |
Rank to Phred conversion table.