A combined alphabet that can hold values of either of its alternatives. More...

#include <seqan3/alphabet/composite/alphabet_variant.hpp>

Inheritance diagram for seqan3::alphabet_variant< alternative_types >:

Public Member Functions
Constructors, destructor and assignment
constexpr	alphabet_variant () noexcept=default
	Defaulted.

constexpr	alphabet_variant (alphabet_variant const &) noexcept=default
	Defaulted.

constexpr	alphabet_variant (alphabet_variant &&) noexcept=default
	Defaulted.

constexpr alphabet_variant &	operator= (alphabet_variant const &) noexcept=default
	Defaulted.

constexpr alphabet_variant &	operator= (alphabet_variant &&) noexcept=default
	Defaulted.

	~alphabet_variant () noexcept=default
	Defaulted.

template<typename alternative_t >
constexpr	alphabet_variant (alternative_t const alternative) noexcept
	Construction via the value of an alternative. More...

template<typename indirect_alternative_t >
constexpr	alphabet_variant (indirect_alternative_t const rhs) noexcept
	Constructor for arguments implicitly convertible to an alternative. More...

template<typename indirect_alternative_t >
constexpr	alphabet_variant (indirect_alternative_t const rhs) noexcept
	Constructor for arguments explicitly (but not implicitly) convertible to an alternative. More...

template<typename indirect_alternative_t >
constexpr alphabet_variant &	operator= (indirect_alternative_t const &rhs) noexcept
	Assignment for arguments assignable to an alternative. More...

Conversion (by index)
template<size_t index>
constexpr bool	holds_alternative () const noexcept
	Whether the variant alphabet currently holds a value of the given alternative. More...

template<size_t index>
constexpr auto	convert_to () const
	Convert to the specified alphabet (throws if holds_alternative() would be false). More...

template<size_t index>
constexpr auto	convert_unsafely_to () const noexcept
	Convert to the specified alphabet (undefined behaviour if holds_alternative() would be false). More...

Conversion (by type)
template<typename alternative_t >
constexpr bool	holds_alternative () const noexcept
	Whether the variant alphabet currently holds a value of the given alternative. More...

template<typename alternative_t >
constexpr alternative_t	convert_to () const
	Convert to the specified alphabet (throws if holds_alternative() would be false). More...

template<typename alternative_t >
constexpr alternative_t	convert_unsafely_to () const noexcept
	Convert to the specified alphabet (undefined behaviour if holds_alternative() would be false). More...

Public Member Functions inherited from seqan3::alphabet_base< alphabet_variant< alternative_types... >,(static_cast< size_t >(alphabet_size< alternative_types >)+...), char >
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. More...

constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet). More...

constexpr alphabet_variant< alternative_types... > &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters. More...

constexpr alphabet_variant< alternative_types... > &	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 chr) noexcept
	Validate whether a character is valid in the combined alphabet. More...

template<typename alternative_t >
static constexpr bool	is_alternative () noexcept
	Returns true if alternative_t is one of the given alternative types. More...

Friends
Comparison operators (against indirect alternatives)
Defines comparison against types that are not subject to implicit construction/conversion but are comparable against alternatives, e.g. `alphabet_variant<seqan3::rna4, seqan3::gap>` vs `alphabet_variant<seqan3::dna4, seqan3::gap>`. Only (in-)equality comparison is defined as reasoning about order of variants is inherently difficult.
template<typename alphabet_variant_t , typename indirect_alternative_type >
constexpr friend auto	operator== (alphabet_variant_t const lhs, indirect_alternative_type const rhs) noexcept -> std::enable_if_t< detail::variant_comparison_guard< alphabet_variant_t, indirect_alternative_type, false, alternative_types... >, bool >
	(In-)Equality comparison against types comparable with alternatives but not convertible to the variant. More...

template<typename alphabet_variant_t , typename indirect_alternative_type >
constexpr friend auto	operator!= (alphabet_variant_t const lhs, indirect_alternative_type const rhs) noexcept -> std::enable_if_t< detail::variant_comparison_guard< alphabet_variant_t, indirect_alternative_type, false, alternative_types... >, bool >
	(In-)Equality comparison against types comparable with alternatives but not convertible to the variant. More...

template<typename alphabet_variant_t , typename indirect_alternative_type , typename = void>
constexpr friend auto	operator== (indirect_alternative_type const lhs, alphabet_variant_t const rhs) noexcept -> std::enable_if_t< detail::variant_comparison_guard< alphabet_variant_t, indirect_alternative_type, true, alternative_types... >, bool >
	(In-)Equality comparison against types comparable with alternatives but not convertible to the variant. More...

template<typename alphabet_variant_t , typename indirect_alternative_type , typename = void>
constexpr friend auto	operator!= (indirect_alternative_type const lhs, alphabet_variant_t const rhs) noexcept -> std::enable_if_t< detail::variant_comparison_guard< alphabet_variant_t, indirect_alternative_type, true, alternative_types... >, bool >
	(In-)Equality comparison against types comparable with alternatives but not convertible to the variant. More...

Comparison operators

Additional Inherited Members
Static Public Attributes inherited from seqan3::alphabet_base< alphabet_variant< alternative_types... >,(static_cast< size_t >(alphabet_size< alternative_types >)+...), char >
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 inherited from seqan3::alphabet_base< alphabet_variant< alternative_types... >,(static_cast< size_t >(alphabet_size< alternative_types >)+...), char >
using	char_type = std::conditional_t< std::same_as< char, void >, char, char >
	The char representation; conditional needed to make semi alphabet definitions legal. More...

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...

Detailed Descriptionstable-api

template<typename ... alternative_types>
class seqan3::alphabet_variant< alternative_types >

A combined alphabet that can hold values of either of its alternatives.

Template Parameters

...alternative_types Types of possible values (at least 2); all must model seqan3::writable_alphabet, std::regular and must be unique; all required functions for seqan3::writable_alphabet need to be callable in a constexpr-context.

The alphabet_variant represents the union of two or more alternative alphabets (e.g. the four letter DNA alternative + the gap alternative). It behaves similar to a variant or std::variant, but it preserves the seqan3::alphabet.

Short description:

combines multiple different alphabets in an "either-or"-fashion;
is itself a seqan3::alphabet;
its alphabet size is the sum of the individual sizes;
default initialises to the the first alternative's default (no empty state like std::variant);
constructible, assignable and (in-)equality-comparable with each alternative type and also all types that these are constructible/assignable/equality-comparable with;
only convertible to its alternatives through the member function convert_to() (which can throw!)

Example

#include <seqan3/alphabet/composite/alphabet_variant.hpp>
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/alphabet/nucleotide/all.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::alphabet_variant<seqan3::dna5, seqan3::gap> letter{};          // implicitly 'A'_dna5
    seqan3::alphabet_variant<seqan3::dna5, seqan3::gap> letter2{'C'_dna5}; // constructed from alternative (== 'C'_dna5)
    seqan3::alphabet_variant<seqan3::dna5, seqan3::gap> letter3{'U'_rna5}; // constructed from type that alternative is constructible from (== 'T'_dna5)
 
    letter2.assign_char('T');                       // == 'T'_dna5
    letter2.assign_char('-');                       // == gap{}
    letter2.assign_char('K');                       // unknown characters map to the default/unknown
                                                    // character of the first alternative type (== 'N'_dna5)
 
    letter2 = seqan3::gap{};                        // assigned from alternative (== gap{})
    letter2 = 'U'_rna5;                             // assigned from type that alternative is assignable from (== 'T'_dna5)
 
    seqan3::dna5 letter4 = letter2.convert_to<seqan3::dna5>();
}

The `char` representation of an alphabet_variant

Part of the seqan3::alphabet concept requires that the alphabet_variant provides a char representation in addition to the rank representation. For an object of seqan3::alphabet_variant, the to_char() member function will always return the same character as if invoked on the respective alternative. In contrast, the assign_char() member function might be ambiguous between the alternative alphabets in a variant.

For example, assigning a '!' to seqan3::dna15 resolves to an object of rank 8 with char representation 'N' while assigning '!' to seqan3::gap always resolves to rank 0, the gap symbol itself ('-'_gap). We tackle this ambiguousness by defaulting unknown characters to the representation of the first alternative (e.g. ‘alphabet_variant<dna15, gap>{}.assign_char(’!')resolves to rank 8, representingN`_dna15).

On the other hand, two alternative alphabets might have the same char representation (e.g if you combine dna4 with dna5, 'A', 'C', 'G' and 'T' are ambiguous). We tackle this ambiguousness by always choosing the first valid char representation (e.g. ‘alphabet_variant<dna4, dna5>{}.assign_char('A’)resolves to rank 0, representing anA`_dna4).

To explicitly assign via the character representation of a specific alphabet, assign to that type first and then assign to the variant, e.g.

#include <seqan3/alphabet/composite/alphabet_variant.hpp>
#include <seqan3/alphabet/nucleotide/all.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::alphabet_variant<seqan3::dna4, seqan3::dna5> var;
    var.assign_char('A');             // will be in the "dna4-state"
    var = 'A'_dna5;                   // will be in the "dna5-state"
}

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

◆ alphabet_variant() [1/3]

template<typename ... alternative_types>

template<typename alternative_t >

constexpr seqan3::alphabet_variant< alternative_types >::alphabet_variant ( alternative_t const alternative )

stable-apiinlineconstexprnoexcept

Construction via the value of an alternative.

Template Parameters

alternative_t One of the alternative types.

Parameters

alternative The value of a alternative that should be assigned.

#include <seqan3/alphabet/composite/alphabet_variant.hpp>
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/alphabet/nucleotide/all.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::alphabet_variant<seqan3::dna4, seqan3::gap> letter1{'C'_dna4}; // or
    seqan3::alphabet_variant<seqan3::dna4, seqan3::gap> letter2 = seqan3::gap{};
}

This entity is stable. Since version 3.1.

◆ alphabet_variant() [2/3]

template<typename ... alternative_types>

template<typename indirect_alternative_t >

constexpr seqan3::alphabet_variant< alternative_types >::alphabet_variant ( indirect_alternative_t const rhs )

experimental-apiinlineconstexprnoexcept

Constructor for arguments implicitly convertible to an alternative.

Template Parameters

indirect_alternative_t A type that is implicitly convertible to an alternative type.

Parameters

rhs	The value that should be assigned.

This constructor is preferred over the explicit version.

Example

#include <seqan3/alphabet/composite/alphabet_variant.hpp>
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/alphabet/nucleotide/all.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::alphabet_variant<seqan3::dna4, seqan3::gap> letter1{'C'_rna4};
    seqan3::alphabet_variant<seqan3::dna4, seqan3::gap> letter2 = 'C'_rna4;
}

seqan3::dna4 and seqan3::rna4 are implicitly convertible to each other so the variant accepts either.
Construction via {} considers implicit and explicit conversions.
Construction via = considers only implicit conversions (but that is sufficient here).

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ alphabet_variant() [3/3]

template<typename ... alternative_types>

template<typename indirect_alternative_t >

constexpr seqan3::alphabet_variant< alternative_types >::alphabet_variant ( indirect_alternative_t const rhs )

experimental-apiinlineexplicitconstexprnoexcept

Constructor for arguments explicitly (but not implicitly) convertible to an alternative.

Template Parameters

indirect_alternative_t A type that is explicitly (but not implicitly) convertible to an alternative type.

Parameters

rhs	The value that should be assigned.

Example

#include <seqan3/alphabet/composite/alphabet_variant.hpp>
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/alphabet/nucleotide/all.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    // possible:
    seqan3::alphabet_variant<seqan3::dna4, seqan3::gap> letter1{'C'_dna5};
    // not possible:
    // seqan3::alphabet_variant<seqan3::dna4, seqan3::gap> letter2 = 'C'_dna5;
}

seqan3::dna4 and seqan3::dna5 are not implicitly convertible to each other, only explicitly.
Construction via {} considers implicit and explicit conversions so this works.
Construction via = considers only implicit conversions so it does not work.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Member Function Documentation

◆ char_is_valid()

template<typename ... alternative_types>

static constexpr bool seqan3::alphabet_variant< alternative_types >::char_is_valid ( char_type const chr )

experimental-apiinlinestaticconstexprnoexcept

Validate whether a character is valid in the combined alphabet.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ convert_to() [1/2]

template<typename ... alternative_types>

template<size_t index>

constexpr auto seqan3::alphabet_variant< alternative_types >::convert_to ( ) const

experimental-apiinlineconstexpr

Convert to the specified alphabet (throws if holds_alternative() would be false).

Template Parameters

index Index of the alternative to check for.

Exceptions

std::bad_variant_access If the variant_alphabet currently holds the value of a different alternative.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ convert_to() [2/2]

template<typename ... alternative_types>

template<typename alternative_t >

constexpr alternative_t seqan3::alphabet_variant< alternative_types >::convert_to ( ) const

experimental-apiinlineconstexpr

Convert to the specified alphabet (throws if holds_alternative() would be false).

Template Parameters

alternative_t The type of the alternative that you wish to check for.

Exceptions

std::bad_variant_access If the variant_alphabet currently holds the value of a different alternative.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ convert_unsafely_to() [1/2]

template<typename ... alternative_types>

template<size_t index>

constexpr auto seqan3::alphabet_variant< alternative_types >::convert_unsafely_to ( ) const

experimental-apiinlineconstexprnoexcept

Convert to the specified alphabet (undefined behaviour if holds_alternative() would be false).

Template Parameters

index Index of the alternative to check for.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ convert_unsafely_to() [2/2]

template<typename ... alternative_types>

template<typename alternative_t >

constexpr alternative_t seqan3::alphabet_variant< alternative_types >::convert_unsafely_to ( ) const

experimental-apiinlineconstexprnoexcept

Convert to the specified alphabet (undefined behaviour if holds_alternative() would be false).

Template Parameters

alternative_t The type of the alternative that you wish to check for.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ holds_alternative() [1/2]

template<typename ... alternative_types>

template<size_t index>

constexpr bool seqan3::alphabet_variant< alternative_types >::holds_alternative ( ) const

experimental-apiinlineconstexprnoexcept

Whether the variant alphabet currently holds a value of the given alternative.

Template Parameters

index Index of the alternative to check for.

See also: std::variant::holds_alternative

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ holds_alternative() [2/2]

template<typename ... alternative_types>

template<typename alternative_t >

constexpr bool seqan3::alphabet_variant< alternative_types >::holds_alternative ( ) const

stable-apiinlineconstexprnoexcept

Whether the variant alphabet currently holds a value of the given alternative.

Template Parameters

alternative_t The type of the alternative that you wish to check for.

This entity is stable. Since version 3.1.

◆ is_alternative()

template<typename ... alternative_types>

template<typename alternative_t >

static constexpr bool seqan3::alphabet_variant< alternative_types >::is_alternative ( )

stable-apiinlinestaticconstexprnoexcept

Returns true if alternative_t is one of the given alternative types.

Template Parameters

alternative_t The type to check.

#include <seqan3/alphabet/composite/alphabet_variant.hpp>
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/alphabet/nucleotide/all.hpp>
#include <gtest/gtest.h>
 
int main()
{
    using variant_t = seqan3::alphabet_variant<seqan3::dna5, seqan3::gap>;
 
    static_assert(variant_t::is_alternative<seqan3::dna5>(), "dna5 is an alternative of variant_t");
    static_assert(!variant_t::is_alternative<seqan3::dna4>(), "dna4 is not an alternative of variant_t");
    static_assert(variant_t::is_alternative<seqan3::gap>(), "gap is an alternative of variant_t");
}

This entity is stable. Since version 3.1.

◆ operator=()

template<typename ... alternative_types>

template<typename indirect_alternative_t >

constexpr alphabet_variant& seqan3::alphabet_variant< alternative_types >::operator= ( indirect_alternative_t const & rhs )

experimental-apiinlineconstexprnoexcept

Assignment for arguments assignable to an alternative.

Template Parameters

indirect_alternative_t A type that one of the alternatives is assignable from.

Parameters

rhs	The value of an alternative.

Most assignments happen through implicit conversion and the default assignment operator. This assignment operator is for the rest.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Friends And Related Function Documentation

◆ operator!= [1/2]

template<typename ... alternative_types>

template<typename alphabet_variant_t , typename indirect_alternative_type >

constexpr friend auto operator!=	(	alphabet_variant_t const	lhs,
		indirect_alternative_type const	rhs
	)		-> std::enable_if_t<detail::variant_comparison_guard<alphabet_variant_t, indirect_alternative_type, false, alternative_types...>, bool>

stable-apifriend

(In-)Equality comparison against types comparable with alternatives but not convertible to the variant.

Template Parameters

alphabet_variant_t	The type of the variant; given as template parameter to prevent conversion.
indirect_alternative_type	Must be comparable with an alternative's type.

Parameters

lhs	Left-hand-side of comparison.
rhs	Right-hand-side of comparison.

Returns: true or false.

To determine (in-)equality, it is first deduced which alternative the argument is comparable with. It is then checked if the variant currently is in that alternative's state and if yes whether the values compare to true; else false is returned.

This entity is stable. Since version 3.1.

◆ operator!= [2/2]

template<typename ... alternative_types>

template<typename alphabet_variant_t , typename indirect_alternative_type , typename = void>

constexpr friend auto operator!=	(	indirect_alternative_type const	lhs,
		alphabet_variant_t const	rhs
	)		-> std::enable_if_t<detail::variant_comparison_guard<alphabet_variant_t, indirect_alternative_type, true, alternative_types...>, bool>

stable-apifriend

(In-)Equality comparison against types comparable with alternatives but not convertible to the variant.

Template Parameters

alphabet_variant_t	The type of the variant; given as template parameter to prevent conversion.
indirect_alternative_type	Must be comparable with an alternative's type.

Parameters

lhs	Left-hand-side of comparison.
rhs	Right-hand-side of comparison.

Returns: true or false.

To determine (in-)equality, it is first deduced which alternative the argument is comparable with. It is then checked if the variant currently is in that alternative's state and if yes whether the values compare to true; else false is returned.

This entity is stable. Since version 3.1.

◆ operator== [1/2]

template<typename ... alternative_types>

template<typename alphabet_variant_t , typename indirect_alternative_type >

constexpr friend auto operator==	(	alphabet_variant_t const	lhs,
		indirect_alternative_type const	rhs
	)		-> std::enable_if_t<detail::variant_comparison_guard<alphabet_variant_t, indirect_alternative_type, false, alternative_types...>, bool>

stable-apifriend

(In-)Equality comparison against types comparable with alternatives but not convertible to the variant.

Template Parameters

alphabet_variant_t	The type of the variant; given as template parameter to prevent conversion.
indirect_alternative_type	Must be comparable with an alternative's type.

Parameters

lhs	Left-hand-side of comparison.
rhs	Right-hand-side of comparison.

Returns: true or false.

To determine (in-)equality, it is first deduced which alternative the argument is comparable with. It is then checked if the variant currently is in that alternative's state and if yes whether the values compare to true; else false is returned.

This entity is stable. Since version 3.1.

◆ operator== [2/2]

template<typename ... alternative_types>

template<typename alphabet_variant_t , typename indirect_alternative_type , typename = void>

constexpr friend auto operator==	(	indirect_alternative_type const	lhs,
		alphabet_variant_t const	rhs
	)		-> std::enable_if_t<detail::variant_comparison_guard<alphabet_variant_t, indirect_alternative_type, true, alternative_types...>, bool>

stable-apifriend

(In-)Equality comparison against types comparable with alternatives but not convertible to the variant.

Template Parameters

alphabet_variant_t	The type of the variant; given as template parameter to prevent conversion.
indirect_alternative_type	Must be comparable with an alternative's type.

Parameters

lhs	Left-hand-side of comparison.
rhs	Right-hand-side of comparison.

Returns: true or false.

To determine (in-)equality, it is first deduced which alternative the argument is comparable with. It is then checked if the variant currently is in that alternative's state and if yes whether the values compare to true; else false is returned.

This entity is stable. Since version 3.1.

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

seqan3/alphabet/composite/alphabet_variant.hpp

Public Member Functions

Static Public Member Functions

Friends

Additional Inherited Members

Detailed Descriptionstable-api

template<typename ... alternative_types> class seqan3::alphabet_variant< alternative_types >

Example

The char representation of an alphabet_variant

Constructor & Destructor Documentation

◆ alphabet_variant() [1/3]

◆ alphabet_variant() [2/3]

Example

◆ alphabet_variant() [3/3]

Example

Member Function Documentation

◆ char_is_valid()

◆ convert_to() [1/2]

◆ convert_to() [2/2]

◆ convert_unsafely_to() [1/2]

◆ convert_unsafely_to() [2/2]

◆ holds_alternative() [1/2]

◆ holds_alternative() [2/2]

◆ is_alternative()

◆ operator=()

Friends And Related Function Documentation

◆ operator!= [1/2]

◆ operator!= [2/2]

◆ operator== [1/2]

◆ operator== [2/2]

template<typename ... alternative_types>
class seqan3::alphabet_variant< alternative_types >

The `char` representation of an alphabet_variant