seqan3::masked< sequence_alphabet_t > Class Template Reference

Implementation of a masked composite, which extends a given alphabet with a mask. More...

#include <seqan3/alphabet/mask/masked.hpp>

Inheritance diagram for seqan3::masked< sequence_alphabet_t >:

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.
Public Member Functions inherited from seqan3::alphabet_tuple_base< masked< sequence_alphabet_t >, sequence_alphabet_t, mask >
constexpr	alphabet_tuple_base (component_types... components) noexcept
	Construction from initialiser-list.
constexpr	alphabet_tuple_base (component_type const alph) noexcept
	Construction via a value of one of the components.
constexpr	alphabet_tuple_base (indirect_component_type const alph) noexcept
	Construction via a value of a subtype that is assignable to one of the components.
constexpr masked< sequence_alphabet_t > &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components.
constexpr masked< sequence_alphabet_t > &	operator= (indirect_component_type const alph) noexcept
	Assignment via a value of a subtype that is assignable to one of the components.
constexpr	operator type () const noexcept
	Implicit cast to a single letter. Works only if the type is unique in the type list.
Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t >
constexpr	alphabet_base () noexcept=default
	Defaulted.
constexpr	alphabet_base (alphabet_base const &) noexcept=default
	Defaulted.
constexpr	alphabet_base (alphabet_base &&) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (alphabet_base const &) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (alphabet_base &&) noexcept=default
	Defaulted.
	~alphabet_base () noexcept=default
	Defaulted.
constexpr char_type	to_char () const noexcept
	Return the letter as a character of char_type.
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).
constexpr derived_type &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters.
constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Static Protected Attributes
static constexpr std::array< rank_type, detail::size_in_values_v< char_type > >	char_to_rank
	Char to rank conversion table.
static constexpr std::array< char_type, alphabet_size >	rank_to_char
	Rank to char conversion table.

Private Types
using	base_t = alphabet_tuple_base< masked< sequence_alphabet_t >, sequence_alphabet_t, mask >
	The base type.

Related Symbols
(Note that these are not member symbols.)
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.
Related Symbols inherited from semialphabet
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.
template<cereal_input_archive archive_t, typename wrapped_alphabet_t >
void	load_minimal (archive_t const &, wrapped_alphabet_t &&l, alphabet_rank_t< detail::strip_cereal_wrapper_t< wrapped_alphabet_t > > const &r)
	Restore an alphabet letter from a saved rank.

Additional Inherited Members
Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t >
static constexpr detail::min_viable_uint_t< size >	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take.
Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t >
using	char_type = std::conditional_t< std::same_as< char_t, void >, char, char_t >
	The char representation; conditional needed to make semi alphabet definitions legal.
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()).

Detailed Description

template<writable_alphabet sequence_alphabet_t>
requires std::regular<sequence_alphabet_t>
class seqan3::masked< sequence_alphabet_t >

Implementation of a masked composite, which extends a given alphabet with a mask.

Template Parameters

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.

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/mask/masked.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::masked<seqan3::dna4> dna4_masked{};
    seqan3::masked<seqan3::dna4> dna4_another_masked{'A'_dna4, seqan3::mask::unmasked};
    // create a dna4 masked alphabet with an unmasked A
 
    dna4_masked.assign_char('a'); // assigns a masked 'A'_dna4
 
    if (dna4_masked.to_char() != dna4_another_masked.to_char())
    {
        seqan3::debug_stream << dna4_masked.to_char() << " is not the same as " << dna4_another_masked.to_char()
                             << "\n";
    }
}

See also

Mask submodule , it contains an explanation of hard-masking (UNKNOWN character) and soft-masking (lower/upper case letters).

This entity is stable. Since version 3.1.

Member Typedef Documentation

char_type

template<writable_alphabet sequence_alphabet_t>

using seqan3::masked< sequence_alphabet_t >::char_type = alphabet_char_t<sequence_alphabet_type>

Equals the char_type of sequence_alphabet_type.

This entity is stable. Since version 3.1.

sequence_alphabet_type

template<writable_alphabet sequence_alphabet_t>

using seqan3::masked< sequence_alphabet_t >::sequence_alphabet_type = sequence_alphabet_t

First template parameter as member type.

This entity is stable. Since version 3.1.

Member Function Documentation

assign_char()

template<writable_alphabet sequence_alphabet_t>

constexpr masked & seqan3::masked< sequence_alphabet_t >::assign_char ( char_type const  c )

inlineconstexprnoexcept

Assign from a character.

This entity is stable. Since version 3.1.

to_char()

template<writable_alphabet sequence_alphabet_t>

constexpr char_type seqan3::masked< sequence_alphabet_t >::to_char ( ) const

inlineconstexprnoexcept

Return a character.

This entity is stable. Since version 3.1.

Member Data Documentation

char_to_rank

template<writable_alphabet sequence_alphabet_t>

constexpr std::array<rank_type, detail::size_in_values_v<char_type> > seqan3::masked< sequence_alphabet_t >::char_to_rank

staticconstexprprotected

Initial value:

{
        []() constexpr
        {
            std::array<rank_type, detail::size_in_values_v<char_type>> ret{};
 
            for (size_t i = 0; i < 256; ++i)
            {
                char_type const c = static_cast<char_type>(i);
 
                ret[i] = is_lower(c) ? seqan3::to_rank(seqan3::assign_char_to(c, sequence_alphabet_type{})) * 2
                                     : seqan3::to_rank(seqan3::assign_char_to(c, sequence_alphabet_type{}));
            }
 
            return ret;
        }()}

Char to rank conversion table.

rank_to_char

template<writable_alphabet sequence_alphabet_t>

constexpr std::array<char_type, alphabet_size> seqan3::masked< sequence_alphabet_t >::rank_to_char

staticconstexprprotected

Initial value:

{
        []() constexpr
        {
            std::array<char_type, alphabet_size> ret{};
 
            for (size_t i = 0; i < alphabet_size; ++i)
            {
                ret[i] = (i < alphabet_size / 2)
                           ? seqan3::to_char(seqan3::assign_rank_to(i, sequence_alphabet_type{}))
                           : to_lower(seqan3::to_char(seqan3::assign_rank_to(i / 2, sequence_alphabet_type{})));
            }
 
            return ret;
        }()}

Rank to char conversion table.

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

• masked.hpp