seqan3::wuss< SIZE > Class Template Reference

The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd... More...

#include <seqan3/alphabet/structure/wuss.hpp>

Inheritance diagram for seqan3::wuss< SIZE >:

Public 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. 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...

Public Member Functions
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...
Constructors, destructor and assignment
constexpr	wuss () noexcept=default
	Defaulted.
constexpr	wuss (wuss const &) noexcept=default
	Defaulted.
constexpr	wuss (wuss &&) noexcept=default
	Defaulted.
constexpr wuss &	operator= (wuss const &) noexcept=default
	Defaulted.
constexpr wuss &	operator= (wuss &&) noexcept=default
	Defaulted.
	~wuss () noexcept=default
Read functions
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...
Write functions
constexpr wuss< 51 > &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...
constexpr wuss< 51 > &	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. More...

Private Types
using	base_t = alphabet_base< wuss< SIZE >, SIZE >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::alphabet_base.
rank_type	rank
	The value of the alphabet letter is stored as the rank.

Static Private Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank
	Char-to-value conversion table. More...
static std::array< int8_t, SIZE > const	interaction_tab
	Lookup table for interactions: unpaired (0), pair-open (< 0), pair-close (> 0). Paired brackets have the same absolute value. More...
static constexpr std::array< char_type, alphabet_size >	rank_to_char
	Value-to-char conversion table. More...

Related Functions
(Note that these are not member functions.)
using	wuss51 = wuss< 51 >
	Alias for the default type wuss51.
Literals
std::vector< wuss51 >	operator""_wuss51 (const char *str, std::size_t len)
	The seqan3::wuss51 string literal. More...
constexpr wuss51	operator""_wuss51 (char const ch) noexcept
	The seqan3::wuss51 char literal. More...
Generic serialisation functions for all seqan3::semialphabet
All types that satisfy seqan3::semialphabet can be serialised via Cereal.
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. More...

RNA structure properties
static constexpr uint8_t	max_pseudoknot_depth {static_cast<uint8_t>((alphabet_size - 7) / 2)}
	The ability of this alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth. It is the number of distinct pairs of interaction symbols the format supports: 4..30 (depends on size)
constexpr bool	is_pair_open () const noexcept
	Check whether the character represents a rightward interaction in an RNA structure. More...
constexpr bool	is_pair_close () const noexcept
	Check whether the character represents a leftward interaction in an RNA structure. More...
constexpr bool	is_unpaired () const noexcept
	Check whether the character represents an unpaired position in an RNA structure. More...
constexpr std::optional< uint8_t >	pseudoknot_id () const noexcept
	Get an identifier for a pseudoknotted interaction, where opening and closing brackets of the same type have the same id. More...

Detailed Description

template<uint8_t SIZE = 51>
class seqan3::wuss< SIZE >

The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd...

Template Parameters

SIZE	The alphabet size defaults to 51 and must be an odd number in range 15..67. It determines the allowed pseudoknot depth by adding characters AaBb..Zz to the alphabet.

The symbols .:,-_~; denote unpaired characters, brackets <>()[]{} represent base pair interactions and AaBbCcDd... form pseudoknots in the structure. The default alphabet has size 51 (letters until Rr). The size can be varied with the optional template parameter between 15 (no letters for pseudoknots) and 67 (all Aa-Zz for pseudoknots).

<<<___>>>,,<<<__>>>
<<<<_AAAA____>>>>aaaa

Usage

The following code example creates a wuss vector, modifies it, and prints the result to stderr.

#include <seqan3/alphabet/structure/wuss.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_wuss51;
 
    // create vector
    std::vector<seqan3::wuss51> vec{'.'_wuss51, '>'_wuss51, '>'_wuss51};
    // modify and print
    vec[1] = '<'_wuss51;
    for (seqan3::wuss51 chr : vec)
        seqan3::debug_stream << seqan3::to_char(chr);  // .<>
    seqan3::debug_stream << "\n";
}

Member Typedef Documentation

char_type

template<uint8_t SIZE = 51>

using seqan3::alphabet_base< derived_type, size, char_t >::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.

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.

This entity is stable. Since version 3.1.

rank_type

template<uint8_t SIZE = 51>

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

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

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

~wuss()

template<uint8_t SIZE = 51>

seqan3::wuss< SIZE >::~wuss ( )

defaultnoexcept

Defaulted.

Member Function Documentation

assign_char()

constexpr wuss< 51 > & seqan3::alphabet_base< wuss< 51 > , size, char >::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.

This entity is stable. Since version 3.1.

assign_rank()

constexpr wuss< 51 > & seqan3::alphabet_base< wuss< 51 > , size, char >::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.

This entity is stable. Since version 3.1.

is_pair_close()

template<uint8_t SIZE = 51>

constexpr bool seqan3::wuss< SIZE >::is_pair_close ( ) const

inlineconstexprnoexcept

Check whether the character represents a leftward interaction in an RNA structure.

Returns

True if the letter represents a leftward interaction, False otherwise.

is_pair_open()

template<uint8_t SIZE = 51>

constexpr bool seqan3::wuss< SIZE >::is_pair_open ( ) const

inlineconstexprnoexcept

Check whether the character represents a rightward interaction in an RNA structure.

Returns

True if the letter represents a rightward interaction, False otherwise.

is_unpaired()

template<uint8_t SIZE = 51>

constexpr bool seqan3::wuss< SIZE >::is_unpaired ( ) const

inlineconstexprnoexcept

Check whether the character represents an unpaired position in an RNA structure.

Returns

True if the letter represents an unpaired site, False otherwise.

pseudoknot_id()

template<uint8_t SIZE = 51>

constexpr std::optional<uint8_t> seqan3::wuss< SIZE >::pseudoknot_id ( ) const

inlineconstexprnoexcept

Get an identifier for a pseudoknotted interaction, where opening and closing brackets of the same type have the same id.

Returns

The pseudoknot id, if alph denotes an interaction, and no value otherwise. It is guaranteed to be smaller than seqan3::max_pseudoknot_depth.

to_char() [1/2]

constexpr char_type seqan3::alphabet_base< wuss< 51 > , size, char >::to_char ( ) const

inlineconstexprnoexceptinherited

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_char() [2/2]

template<uint8_t SIZE = 51>

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

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() [1/2]

constexpr rank_type seqan3::alphabet_base< wuss< 51 > , size, char >::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.

This entity is stable. Since version 3.1.

to_rank() [2/2]

template<uint8_t SIZE = 51>

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

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 Function Documentation

operator""_wuss51() [1/2]

template<uint8_t SIZE = 51>

constexpr wuss51 operator""_wuss51 ( char const  ch )

related

The seqan3::wuss51 char literal.

Parameters

[in]

ch

The character to represent as wuss.

Returns

seqan3::wuss51

You can use this string literal to assign a seqan3::wuss51 character. For different wuss alphabet sizes the assign_char function must be used.

#include <seqan3/alphabet/structure/wuss.hpp>
 
int main()
{
    using seqan3::operator""_wuss51;
 
    // Using the char literal to assign a single WUSS character:
    seqan3::wuss51 my_letter{'~'_wuss51};
    
    my_letter.assign_char('<'); // <- assigns the char explicitly
}

operator""_wuss51() [2/2]

template<uint8_t SIZE = 51>

std::vector< wuss51 > operator""_wuss51 ( const char *  str, std::size_t  len  )

related

The seqan3::wuss51 string literal.

Parameters

[in]	str	A pointer to the character string to assign.
[in]	len	The size of the character string to assign.

Returns

std::vector<seqan3::wuss51>

You can use this string literal to easily assign to a vector of seqan3::wuss51 characters:

#include <seqan3/alphabet/structure/wuss.hpp>
 
int main()
{
    using seqan3::operator""_wuss51;
 
    // Using the string literal to assign a vector of WUSS characters:
    std::vector<seqan3::wuss<>> foo{".<..>."_wuss51};
    std::vector<seqan3::wuss<>> bar = ".<..>."_wuss51;
    auto bax = ".<..>."_wuss51;
}

save_minimal()

template<cereal_output_archive archive_t, semialphabet alphabet_t>

alphabet_rank_t< alphabet_t > save_minimal ( archive_t const &  , alphabet_t const &  l  )

related

Save an alphabet letter to stream.

Template Parameters

archive_t	Must satisfy seqan3::cereal_output_archive.
alphabet_t	Type of l; must satisfy seqan3::semialphabet.

Parameters

l	The alphabet letter.

Delegates to seqan3::to_rank.

Attention

These functions are never called directly, see the Alphabet module on how to use serialisation.

This entity is stable. Since version 3.1.

Member Data Documentation

alphabet_size

template<uint8_t SIZE = 51>

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< derived_type, size, char_t >::alphabet_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.

char_to_rank

template<uint8_t SIZE = 51>

constexpr std::array<rank_type, 256> seqan3::wuss< SIZE >::char_to_rank

staticconstexprprivate

Initial value:

{
        [] () constexpr
        {
            std::array<rank_type, 256> rank_table{};
 
            
            for (rank_type & rnk : rank_table)
                rnk = 6u;
 
            
            for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
                rank_table[rank_to_char[rnk]] = rnk;
            return rank_table;
        } ()
    }

Char-to-value conversion table.

interaction_tab

template<uint8_t SIZE>

constexpr std::array< int8_t, SIZE > seqan3::wuss< SIZE >::interaction_tab

staticconstexprprivate

Initial value:

= [] () constexpr
{
    std::array<int8_t, alphabet_size> interaction_table{};
    int cnt_open = 0;
    int cnt_close = 0;
 
    for (rank_type rnk = 0u; rnk <= 6u; ++rnk)
    {
        interaction_table[rnk] = 0;
    }
 
    for (rank_type rnk = 7u; rnk <= 10u; ++rnk)
    {
        interaction_table[rnk] = --cnt_open;
    }
 
    for (rank_type rnk = 11u; rnk <= 14u; ++rnk)
    {
        interaction_table[rnk] = ++cnt_close;
    }
 
    for (rank_type rnk = 15u; rnk + 1u < alphabet_size; rnk += 2u)
    {
        interaction_table[rnk]      = --cnt_open;
        interaction_table[rnk + 1u] = ++cnt_close;
    }
 
    return interaction_table;
} ()

Lookup table for interactions: unpaired (0), pair-open (< 0), pair-close (> 0). Paired brackets have the same absolute value.

rank_to_char

template<uint8_t SIZE = 51>

constexpr std::array<char_type, alphabet_size> seqan3::wuss< SIZE >::rank_to_char

staticconstexprprivate

Initial value:

{
        [] () constexpr
        {
            std::array<char_type, alphabet_size> chars
            {
                '.', ':', ',', '-', '_', '~', ';', '<', '(', '[', '{', '>', ')', ']', '}'
            };
 
            
            for (rank_type rnk = 15u; rnk + 1u < alphabet_size; rnk += 2u)
            {
                char_type const off = static_cast<char_type>((rnk - 15u) / 2u);
                chars[rnk] = 'A' + off;
                chars[rnk + 1u] = 'a' + off;
            }
 
            return chars;
        } ()
    }

Value-to-char conversion table.

---

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

• seqan3/alphabet/structure/wuss.hpp