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 ()
	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.

constexpr	masked (component_type const alph)
	Construction via a value of one of the components. More...

constexpr	masked (indirect_component_type const alph)
	Construction via a value of a subtype that is assignable to one of the components. More...

constexpr masked &	operator= (component_type const alph)
	Assignment via a value of one of the components. More...

constexpr masked &	operator= (indirect_component_type const alph)
	Assignment via a value of a subtype that is assignable to one of the components. More...

Write functions
constexpr masked &	assign_char (char_type const c) noexcept
	Assign from a character.

masked &	assign_char_strictly (char_type const c)
	Strict 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.

Comparison operators (against indirect component_list)
`*this` is cast to the component type before comparison. (These overloads enable comparison for all types that a component type is comparable with).
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 value has a one-to-one mapping to an alphabet value. More...

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 >
	masked (sequence_alphabet_type &&, mask const &) -> masked< std::decay_t< sequence_alphabet_type >>
	Type deduction guide enables usage of masked without specifying template args. More...

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...

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...

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...

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< masked< sequence_alphabet_t >, component_types... > const rhs) noexcept

constexpr bool	operator!= (indirect_component_type const lhs, alphabet_tuple_base< masked< sequence_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator< (indirect_component_type const lhs, alphabet_tuple_base< masked< sequence_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator> (indirect_component_type const lhs, alphabet_tuple_base< masked< sequence_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator<= (indirect_component_type const lhs, alphabet_tuple_base< masked< sequence_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator>= (indirect_component_type const lhs, alphabet_tuple_base< masked< sequence_alphabet_t >, indirect_component_types... > const rhs) noexcept

Detailed Description

template<typename 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::Semialphabet.
mask_t	Types of masked letter; must satisfy seqan3::Semialphabet, defaults to seqan3::mask.

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.

masked<dna4> dna4_masked{};
masked<dna4> dna4_another_masked{'A'_dna4, 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())
    debug_stream << dna4_masked.to_char() << " is not the same as " << dna4_another_masked.to_char() << "\n";

Constructor & Destructor Documentation

◆ masked() [1/2]

template<typename sequence_alphabet_t >

constexpr seqan3::masked< sequence_alphabet_t >::masked ( component_type const alph )

inline

Construction via a value of one of the components.

Template Parameters

component_type Must be one uniquely contained in the type list of the composite.

Parameters

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).

qualified<dna4, phred42> letter1{'C'_dna4}; // creates {'C'_dna4, phred42{0}}

qualified<dna4, phred42> letter2{phred42{1}}; // creates {'A'_dna4, phred42{1}}

◆ masked() [2/2]

template<typename sequence_alphabet_t >

constexpr seqan3::masked< sequence_alphabet_t >::masked ( indirect_component_type const alph )

inline

Construction via a value of a subtype that is assignable to one of the components.

Template Parameters

indirect_component_type Type that models seqan3::WeaklyAssignable for one of the component types.

Parameters

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).

// The following creates {'C'_dna4, phre42{0}}
qualified<dna4, phred42> letter1{'C'_dna4};
// The following also creates {'C'_dna4, phred42{0}}, since rna4 assignable to dna4
qualified<dna4, phred42> letter2{'C'_rna4};
if (letter1 == letter2)
    debug_stream << "yeah\n"; // yeah

Member Function Documentation

◆ assign_rank()

template<typename derived_type, size_t size, typename char_t = char>

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_rank ( rank_type const c )

inlinenoexceptinherited

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.

◆ char_is_valid()

template<typename sequence_alphabet_t >

static constexpr bool seqan3::masked< sequence_alphabet_t >::char_is_valid ( char_type const c )

inlinestaticnoexcept

Validate whether a character value has a one-to-one mapping to an alphabet value.

Satisfies the seqan3::Semialphabet::char_is_valid_for() requirement via the seqan3::char_is_valid_for() wrapper.

Default implementation: True for all character values that are reproduced by to_char() after being assigned to the alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ operator=() [1/2]

template<typename sequence_alphabet_t >

constexpr masked& seqan3::masked< sequence_alphabet_t >::operator= ( component_type const alph )

inline

Assignment via a value of one of the components.

Template Parameters

component_type One of the component types. Must be uniquely contained in the type list of the composite.

Parameters

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).

qualified<dna4, phred42> letter1{'T'_dna4, phred42{1}};
letter1 = 'C'_dna4; // yields {'C'_dna4, phred42{1}}
letter1 = phred42{2}; // yields {'C'_dna4, phred42{2}}

◆ operator=() [2/2]

template<typename sequence_alphabet_t >

constexpr masked& seqan3::masked< sequence_alphabet_t >::operator= ( indirect_component_type const alph )

inline

Assignment via a value of a subtype that is assignable to one of the components.

Template Parameters

indirect_component_type Type that models seqan3::WeaklyAssignable for one of the component types.

Parameters

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).

qualified<dna4, phred42> letter1{'T'_dna4, phred42{1}};
letter1 = 'C'_rna4; // yields {'C'_dna4, phred42{1}}

◆ to_rank()

template<typename derived_type, size_t size, typename char_t = char>

constexpr rank_type seqan3::alphabet_base< derived_type, size, char_t >::to_rank ( ) const

inlinenoexceptinherited

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.

Friends And Related Function Documentation

◆ masked()

template<typename sequence_alphabet_type >

masked	(	sequence_alphabet_type &&	,
		mask const &
	)		-> masked< std::decay_t< sequence_alphabet_type >>

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

seqan3/alphabet/mask/masked.hpp

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Related Functions

Detailed Description

template<typename sequence_alphabet_t> class seqan3::masked< sequence_alphabet_t >

Constructor & Destructor Documentation

◆ masked() [1/2]

◆ masked() [2/2]

Member Function Documentation

◆ assign_rank()

Complexity

Exceptions

◆ char_is_valid()

Complexity

Exceptions

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ to_rank()

Complexity

Exceptions

Friends And Related Function Documentation

◆ masked()

template<typename sequence_alphabet_t>
class seqan3::masked< sequence_alphabet_t >