Implementation of a masked composite, which extends a given alphabet with a mask. More...
#include <seqan3/alphabet/mask/masked.hpp>
Public Types | |
using | char_type = alphabet_char_t< sequence_alphabet_type > |
Equals the char_type of sequence_alphabet_type. | |
using | sequence_alphabet_type = sequence_alphabet_t |
First template parameter as member type. | |
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | masked ()=default |
Defaulted. | |
constexpr | masked (masked const &)=default |
Defaulted. | |
constexpr | masked (masked &&)=default |
Defaulted. | |
constexpr masked & | operator= (masked const &)=default |
Defaulted. | |
constexpr masked & | operator= (masked &&)=default |
Defaulted. | |
~masked ()=default | |
Defaulted. | |
Write functions | |
constexpr masked & | assign_char (char_type const c) noexcept |
Assign from a character. | |
Read functions | |
constexpr char_type | to_char () const noexcept |
Return a character. | |
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 masked< sequence_alphabet_t > & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr masked< sequence_alphabet_t > & | assign_rank (rank_type const c) noexcept |
Assign from a numeric value. More... | |
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... | |
Static Protected Attributes | |
static constexpr std::array< rank_type, detail::size_in_values_v< char_type > > | char_to_rank |
Char to rank conversion table. More... | |
static constexpr std::array< char_type, alphabet_size > | rank_to_char |
Rank to char conversion table. More... | |
Private Types | |
using | base_t = alphabet_tuple_base< masked< sequence_alphabet_t >, sequence_alphabet_t, mask > |
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 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 > | |
masked (sequence_alphabet_type &&, mask const &) -> masked< std::decay_t< sequence_alphabet_type >> | |
Type deduction guide enables usage of masked 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... | |
Implementation of a masked composite, which extends a given alphabet with a mask.
sequence_alphabet_t | Type of the first letter; must satisfy seqan3::writable_alphabet and std::regular. |
The masked composite represents a seqan3::alphabet_tuple_base of any given alphabet with the masked alphabet. It allows one to specify which portions of a sequence should be masked, without losing additional information by replacing the sequence directly.
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protectedinherited |
The type of the alphabet when represented as a number (e.g. via to_rank()).
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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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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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staticconstexprprotected |
Char to rank conversion table.
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privateinherited |
Befriend the derived type so that it can instantiate.
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staticconstexprprotected |
Rank to char conversion table.