The actual implementation of seqan3::cigar::operation for documentation purposes only. More...

#include <seqan3/alphabet/cigar/exposition_only/cigar_operation.hpp>

Inheritance diagram for seqan3::exposition_only::cigar_operation:

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

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

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

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

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

	~cigar_operation () noexcept=default
	Defaulted.

Public Member Functions inherited from seqan3::alphabet_base< cigar_operation, 9, 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.

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

constexpr cigar_operation &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters.

constexpr cigar_operation &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Private Types
using	base_t = alphabet_base< cigar_operation, 9, char >
	The base class.

Static Private Member Functions
static constexpr rank_type	char_to_rank (char_type const chr)
	Returns the rank representation of character.

static constexpr char_type	rank_to_char (rank_type const rank)
	Returns the character representation of rank.

Private Attributes
friend	base_t
	Befriend seqan3::alphabet_base.

Static Private Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank_table
	The lookup table used in char_to_rank.

static constexpr char_type	rank_to_char_table [alphabet_size] {'M', 'D', 'I', 'S', 'H', 'N', 'P', 'X', '='}
	The lookup table used in rank_to_char.

Additional Inherited Members
Static Public Attributes inherited from seqan3::alphabet_base< cigar_operation, 9, 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.

Protected Types inherited from seqan3::alphabet_base< cigar_operation, 9, 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.

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 Symbols inherited from semialphabet
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.

template<cereal_input_archive archive_t, typename wrapped_alphabet_t >
void	load_minimal (archive_t const &, wrapped_alphabet_t &&l, alphabet_rank_t< detail::strip_cereal_wrapper_t< wrapped_alphabet_t > > const &r)
	Restore an alphabet letter from a saved rank.

Detailed Descriptionno-api

The actual implementation of seqan3::cigar::operation for documentation purposes only.

Note: This class only exists because of technical reasons, please always use seqan3::cigar::operation instead of seqan3::exposition_only::cigar_operation.; We cannot declare seqan3::cigar::operation in-class, because we need to specify the second tuple element of seqan3::alphabet_tuple_base before we actually can declare it in-class. This is a trade-off to make seqan3::cigar a non-template class.

See also: seqan3::exposition_only for an explanation on exposition-only.

This entity is not part of the SeqAn API. Do not rely on it in your applications. Please always use seqan3::cigar::operation. The API-Stability of all members documented in this class applies directly to seqan3::cigar::operation.

Member Function Documentation

◆ char_to_rank() [no-api]

static constexpr rank_type seqan3::exposition_only::cigar_operation::char_to_rank ( char_type const chr )

no-apiinlinestaticconstexprprivate

Returns the rank representation of character.

This function is required by seqan3::alphabet_base.

◆ rank_to_char() [no-api]

static constexpr char_type seqan3::exposition_only::cigar_operation::rank_to_char ( rank_type const rank )

no-apiinlinestaticconstexprprivate

Returns the character representation of rank.

This function is required by seqan3::alphabet_base.

Member Data Documentation

◆ char_to_rank_table [no-api]

constexpr std::array<rank_type, 256> seqan3::exposition_only::cigar_operation::char_to_rank_table

no-apistaticconstexprprivate

Initial value:

{[]() constexpr
                                                                   {
                                                                       std::array<rank_type, 256> ret{};
 
                                                                       
                                                                       for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
                                                                       {
                                                                           ret[rank_to_char_table[rnk]] = rnk;
                                                                       }
 
                                                                       return ret;
                                                                   }()}

The lookup table used in char_to_rank.

We would have defined these lookup tables directly within their respective constexpr functions, but at the time of writing this, gcc did not (clang >= 4 did!) auto-generate lookup tables.

static constexpr char_type rank_to_char(rank_type const rank)
{
    // not possible because of static not being allowed within a constexpr function
    static constexpr lookup_table = ...;
    return lookup_table[rank];
}
 
static constexpr char_type rank_to_char(rank_type const rank)
{
    // up-to the compiler to optimise, no guarantee that a lookup table is used.
    constexpr lookup_table = ...;
    return lookup_table[rank];
}

See also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99320 for the progress on gcc

◆ rank_to_char_table [no-api]

constexpr char_type seqan3::exposition_only::cigar_operation::rank_to_char_table[alphabet_size] {'M', 'D', 'I', 'S', 'H', 'N', 'P', 'X', '='}

no-apistaticconstexprprivate

The lookup table used in rank_to_char.

We would have defined these lookup tables directly within their respective constexpr functions, but at the time of writing this, gcc did not (clang >= 4 did!) auto-generate lookup tables.

static constexpr char_type rank_to_char(rank_type const rank)
{
    // not possible because of static not being allowed within a constexpr function
    static constexpr lookup_table = ...;
    return lookup_table[rank];
}
 
static constexpr char_type rank_to_char(rank_type const rank)
{
    // up-to the compiler to optimise, no guarantee that a lookup table is used.
    constexpr lookup_table = ...;
    return lookup_table[rank];
}

See also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99320 for the progress on gcc

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

cigar_operation.hpp

Public Member Functions

Private Types

Static Private Member Functions

Private Attributes

Static Private Attributes