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.
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.

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()).

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...

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.

Detailed Description

template<writable_alphabet 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.

#include <seqan3/alphabet/mask/masked.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_dna4;
 
    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";
    }
}

Member Function Documentation

assign_char()

constexpr masked< sequence_alphabet_t > & seqan3::alphabet_base< masked< sequence_alphabet_t > , size, void >::assign_char ( char_type const  c )

inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters

c	The character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

assign_rank()

constexpr masked< sequence_alphabet_t > & seqan3::alphabet_base< masked< sequence_alphabet_t > , size, void >::assign_rank ( rank_type const  c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_rank()

constexpr rank_type seqan3::alphabet_base< masked< sequence_alphabet_t > , size, void >::to_rank ( ) const

inlineconstexprnoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

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:

{
        [] ()
        {
            std::array<rank_type, detail::size_in_values_v<char_type>> ret{};
 
            for (size_t i = 0; i < 256; ++i)
            {
                char_type 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:

{
        [] ()
        {
            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:

• seqan3/alphabet/mask/masked.hpp