A CRTP-base that makes defining a custom alphabet easier. More...

#include <seqan3/alphabet/alphabet_base.hpp>

Inheritance diagram for seqan3::alphabet_base< derived_type, size, char_t >:

Public Member Functions
Constructors, destructor and assignment
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.

Read functions
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).

Write functions
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 Public Attributes
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
Member types
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()).

Friends
Comparison operators
constexpr bool	operator== (derived_type const lhs, derived_type const rhs) noexcept
	Checks whether the letters `lhs` and `rhs` are equal.

constexpr bool	operator!= (derived_type const lhs, derived_type const rhs) noexcept
	Checks whether the letters `lhs` and `rhs` are unequal.

constexpr bool	operator< (derived_type const lhs, derived_type const rhs) noexcept
	Checks whether the letter `lhs` is smaller than `rhs`.

constexpr bool	operator> (derived_type const lhs, derived_type const rhs) noexcept
	Checks whether the letter `lhs` is greater than `rhs`.

constexpr bool	operator<= (derived_type const lhs, derived_type const rhs) noexcept
	Checks whether the letter `lhs` is smaller than or equal to `rhs`.

constexpr bool	operator>= (derived_type const lhs, derived_type const rhs) noexcept
	Checks whether the letter `lhs` is bigger than or equal to `rhs`.

Detailed Description

template<typename derived_type, size_t size, typename char_t = char>
class seqan3::alphabet_base< derived_type, size, char_t >

A CRTP-base that makes defining a custom alphabet easier.

Template Parameters

derived_type	The CRTP parameter type.
size	The size of the alphabet.
char_t	The character type of the alphabet (set this to `void` when defining just a seqan3::semialphabet).

You can use this class to define your own alphabet, but types are not required to be based on it to model seqan3::alphabet, it is purely a way to avoid code duplication.

The base class represents the alphabet value as the rank and automatically deduces the rank type from the size and defines all required member functions. The derived type needs to define only the following two static member functions (can be private if the base class is befriended):

static constexpr char_type rank_to_char(rank_type const rank); that defines for every possible rank value the corresponding char value. (The implementation can be a lookup-table or an arithmetic expression.)
static constexpr rank_type char_to_rank(char_type const chr); that defines for every possible character value the corresponding rank value (adapt size if char_type isn't char). (The implementation can be a lookup-table or an arithmetic expression.)

Example

This creates an alphabet called ab which has size two and the two letters 'A' and 'B':

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/alphabet_base.hpp>
#include <seqan3/alphabet/concept.hpp>
#include <seqan3/utility/char_operations/transform.hpp> // seqan3::to_lower
 
class ab : public seqan3::alphabet_base<ab, 2>
{
private:
    // make the base class a friend so it can access the tables:
    friend alphabet_base<ab, 2>;
 
    // This function is expected by seqan3::alphabet_base
    static constexpr char_type rank_to_char(rank_type const rank)
    {
        // via a lookup table
        return rank_to_char_table[rank];
        // or via an arithmetic expression
        return rank == 1 ? 'B' : 'A';
    }
 
    // This function is expected by seqan3::alphabet_base
    static constexpr rank_type char_to_rank(char_type const chr)
    {
        // via a lookup table
        using index_t = std::make_unsigned_t<char_type>;
        return char_to_rank_table[static_cast<index_t>(chr)];
        // or via an arithmetic expression
        return seqan3::to_lower(chr) == 'b' ? 1 : 0;
    }
 
private:
    // === lookup-table implementation detail ===
 
    // map 0 -> A and 1 -> B
    static constexpr std::array<char_type, alphabet_size> rank_to_char_table{'A', 'B'};
 
    // map every letter to rank zero, except Bs
    static constexpr std::array<rank_type, 256> char_to_rank_table{
        // initialise with an immediately evaluated lambda expression:
        []()
        {
            std::array<rank_type, 256> ret{}; // initialise all values with 0 / 'A'
 
            // only 'b' and 'B' result in rank 1
            ret['b'] = 1;
            ret['B'] = 1;
 
            return ret;
        }()};
};
 
// The class ab satisfies the alphabet concept.
static_assert(seqan3::alphabet<ab>);
static_assert(seqan3::writable_alphabet<ab>);

This entity is stable. Since version 3.1.

Member Typedef Documentation

◆ char_type

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

using seqan3::alphabet_base< derived_type, size, char_t >::char_type = std::conditional_t<std::same_as<char_t, void>, char, char_t>

protected

The char representation; conditional needed to make semi alphabet definitions legal.

We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t is void.

Attention: Please use seqan3::alphabet_char_t to access this type.

This entity is stable. Since version 3.1.

◆ rank_type

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

using seqan3::alphabet_base< derived_type, size, char_t >::rank_type = detail::min_viable_uint_t<size - 1>

protected

The type of the alphabet when represented as a number (e.g. via to_rank()).

Attention: Please use seqan3::alphabet_rank_t to access this type.

This entity is stable. Since version 3.1.

Member Function Documentation

◆ assign_char()

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

constexpr derived_type & seqan3::alphabet_base< derived_type, size, char_t >::assign_char ( char_type const chr )

inlineconstexprnoexcept

Assign from a character, implicitly converts invalid characters.

Parameters

chr	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.

This entity is stable. Since version 3.1.

◆ 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 )

inlineconstexprnoexcept

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.

This entity is stable. Since version 3.1.

◆ to_char()

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

constexpr char_type seqan3::alphabet_base< derived_type, size, char_t >::to_char ( ) const

inlineconstexprnoexcept

Return the letter as a character of char_type.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

◆ 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

inlineconstexprnoexcept

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.

This entity is stable. Since version 3.1.

Friends And Related Symbol Documentation

◆ operator!=

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

constexpr bool operator!=	(	derived_type const	lhs,
		derived_type const	rhs
	)

friend

Checks whether the letters lhs and rhs are unequal.

This entity is stable. Since version 3.1.

◆ operator<

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

constexpr bool operator<	(	derived_type const	lhs,
		derived_type const	rhs
	)

friend

Checks whether the letter lhs is smaller than rhs.

This entity is stable. Since version 3.1.

◆ operator<=

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

constexpr bool operator<=	(	derived_type const	lhs,
		derived_type const	rhs
	)

friend

Checks whether the letter lhs is smaller than or equal to rhs.

This entity is stable. Since version 3.1.

◆ operator==

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

constexpr bool operator==	(	derived_type const	lhs,
		derived_type const	rhs
	)

friend

Checks whether the letters lhs and rhs are equal.

This entity is stable. Since version 3.1.

◆ operator>

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

constexpr bool operator>	(	derived_type const	lhs,
		derived_type const	rhs
	)

friend

Checks whether the letter lhs is greater than rhs.

This entity is stable. Since version 3.1.

◆ operator>=

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

constexpr bool operator>=	(	derived_type const	lhs,
		derived_type const	rhs
	)

friend

Checks whether the letter lhs is bigger than or equal to rhs.

This entity is stable. Since version 3.1.

Member Data Documentation

◆ alphabet_size

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

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< derived_type, size, char_t >::alphabet_size = size

staticconstexpr

The size of the alphabet, i.e. the number of different values it can take.

This entity is stable. Since version 3.1.

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

alphabet_base.hpp

Public Member Functions

Static Public Attributes

Protected Types

Friends

Detailed Description

Example

Member Typedef Documentation

◆ char_type

◆ rank_type

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_rank()

Complexity

Exceptions

◆ to_char()

Complexity

Exceptions

◆ to_rank()

Complexity

Exceptions

Friends And Related Symbol Documentation

◆ operator!=

◆ operator<

◆ operator<=

◆ operator==

◆ operator>

◆ operator>=

Member Data Documentation

◆ alphabet_size