The cigar semialphabet pairs a counter with a bio::alphabet::cigar_op letter. More...

#include <bio/alphabet/cigar/cigar.hpp>

Inheritance diagram for bio::alphabet::cigar:

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

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

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

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

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

	~cigar () noexcept=default
	Defaulted.

constexpr	cigar (uint32_t const count, cigar_op op) noexcept
	Construct from component types.

constexpr	cigar (uint32_t const count) noexcept
	Construct from one component.

constexpr	cigar (cigar_op const op) noexcept
	Construct from one component.

constexpr cigar &	operator= (uint32_t const count) noexcept
	Assign from one component.

constexpr cigar &	operator= (cigar_op const op) noexcept
	Assign from one component.

Read functions
constexpr uint32_t	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).

constexpr	operator uint32_t () const
	Convert to number-component.

constexpr	operator cigar_op () const
	Convert to bio::alphabet::cigar_op component.

std::string_view	to_string (std::span< char > buffer) const noexcept
	Convert to string representation.

ranges::small_string< 10 >	to_string () const noexcept
	Convert to string representation.

Write functions
constexpr cigar &	assign_rank (uint32_t const r) noexcept
	Assign from a numeric value.

cigar &	assign_string (std::string_view const s)
	Assign from the string representation.

Friends
Get functions
template<meta::one_of< uint32_t, cigar_op > type>
constexpr type	get (cigar const &l) noexcept
	Get one of the two components from the cigar element (by type).

template<meta::one_of< uint32_t, cigar_op > type>
constexpr auto	get (cigar &l) noexcept
	Get one of the two components from the cigar element (by type).

template<size_t index> requires (index == 0 \|\| index == 1)
constexpr auto	get (cigar const &l) noexcept
	Get one of the two components from the cigar element (by index).

template<size_t index> requires (index == 0 \|\| index == 1)
constexpr auto	get (cigar &l) noexcept
	Get one of the two components from the cigar element (by index).

Detailed Description

The cigar semialphabet pairs a counter with a bio::alphabet::cigar_op letter.

This semialphabet represents a unit in a CIGAR string, typically found in the SAM and BAM formats. It consists of two components, representing a number and symbol. These components are implemented as uint32_t and bio::alphabet::cigar_op, however, only values [0, 2^28) are valid for the number component.

It has a "visual representation", but since this is a string and not a char, the type only models bio::alphabet::writable_semialphabet and not bio::alphabet::writable_alphabet. Members for reading/writing the string are provided.

To avoid confusion between string and char literal, this alphabet has no user defined literal operators. Always assign from a pair of uint32_t and bio::alphabet::cigar_op.

ABI

Objects of this type always occupy exactly 32bits of memory.

On little-endian CPU architectures (all platforms officially supported by BioC++), objects of this type are guaranteed to have the same binary representation as CIGAR elements in BAM files.

Example

#include <bio/alphabet/cigar/cigar.hpp>
#include <bio/alphabet/fmt.hpp>
 
using namespace bio::alphabet::literals;
 
int main()
{
    bio::alphabet::cigar c{13, 'M'_cigar_op};
    fmt::print("{}\n", c); // "13M"
 
    c.assign_string("14X");
    fmt::print("{}\n", c); // "14X"
}

Member Function Documentation

◆ assign_rank()

constexpr cigar & bio::alphabet::cigar::assign_rank ( uint32_t const r )

inlineconstexprnoexcept

Assign from a numeric value.

Parameters

r	The rank to be assigned.

This overload overrides the base class's function to ensure correct binary layout.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_string()

cigar & bio::alphabet::cigar::assign_string ( std::string_view const s )

inline

Assign from the string representation.

Parameters

s	The string to assign from.

Exceptions

std::invalid_argument	If the string does not begin with an integer.
bio::alphabet::invalid_char_assignment	If the string does not end on a valid character for bio::alphabet::cigar_op.

◆ to_rank()

constexpr uint32_t bio::alphabet::cigar::to_rank ( ) const

inlineconstexprnoexcept

Return the letter's numeric value (rank in the alphabet).

This overload overrides the base class's function to ensure correct binary layout.

Complexity

Constant.

In contrast to most alphabets, this function has more overhead than just returning the stored value.

Exceptions

Guaranteed not to throw.

◆ to_string()

std::string_view bio::alphabet::cigar::to_string ( std::span< char > buffer ) const

inlinenoexcept

Convert to string representation.

Parameters

[in,out] buffer The place the string will be created in.

Returns: A string_view into the buffer with the string-representation.

This overload takes a character buffer that the string will be created in. The buffer is required to be large enough to hold the string representation; it is recommended to always pass a buffer of at least 10 characters! This is the maximum width of the string.

A string_view into the buffer is returned. This is the only way to know the size of the "string", so you should not discard the return-result. No 0-terminator is written into the buffer.

Friends And Related Function Documentation

◆ get [1/4]

template<meta::one_of< uint32_t, cigar_op > type>

constexpr auto get ( cigar & l )

friend

Get one of the two components from the cigar element (by type).

Template Parameters

type	Return the element of specified type; eith `uint32_t` or bio::alphabet::cigar_op.

Returns: A proxy to the contained element that models the same alphabet concepts and supports assignment.

Example

#include <bio/alphabet/cigar/cigar.hpp>
#include <bio/alphabet/cigar/cigar_op.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::cigar letter{10, 'M'_cigar_op};
 
    uint32_t size{get<uint32_t>(letter)};                 // Note this is equivalent to get<0>(letter)
    bio::alphabet::cigar_op cigar_char{get<bio::alphabet::cigar_op>(letter)}; // Note this is equivalent to get<1>(letter)
 
    fmt::print("Size is {}\n", size);
    fmt::print("Cigar char is {}\n", cigar_char);
 
}

◆ get [2/4]

template<size_t index>
requires (index == 0 || index == 1)

constexpr auto get ( cigar & l )

friend

Get one of the two components from the cigar element (by index).

Template Parameters

index Return the element of specified index; either 0 or 1.

Returns: A proxy to the contained element that models the same alphabet concepts and supports assignment.

Example

#include <bio/alphabet/cigar/cigar.hpp>
#include <bio/alphabet/cigar/cigar_op.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::cigar letter{10, 'M'_cigar_op};
 
    uint32_t size{get<0>(letter)};                // Note this is equivalent to get<uint32_t>(letter)
    bio::alphabet::cigar_op cigar_char{get<1>(letter)};     // Note this is equivalent to get<bio::alphabet::cigar_op>(letter)
 
    fmt::print("Size is {}\n", size);
    fmt::print("Cigar char is {}\n", cigar_char);
 
}

◆ get [3/4]

template<meta::one_of< uint32_t, cigar_op > type>

constexpr type get ( cigar const & l )

friend

Get one of the two components from the cigar element (by type).

Template Parameters

type	Return the element of specified type; eith `uint32_t` or bio::alphabet::cigar_op.

Returns: A object of the requested type.

Example

#include <bio/alphabet/cigar/cigar.hpp>
#include <bio/alphabet/cigar/cigar_op.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::cigar letter{10, 'M'_cigar_op};
 
    uint32_t size{get<uint32_t>(letter)};                 // Note this is equivalent to get<0>(letter)
    bio::alphabet::cigar_op cigar_char{get<bio::alphabet::cigar_op>(letter)}; // Note this is equivalent to get<1>(letter)
 
    fmt::print("Size is {}\n", size);
    fmt::print("Cigar char is {}\n", cigar_char);
 
}

◆ get [4/4]

template<size_t index>
requires (index == 0 || index == 1)

constexpr auto get ( cigar const & l )

friend

Get one of the two components from the cigar element (by index).

Template Parameters

index Return the element of specified index; either 0 or 1.

Returns: A object of the requested type.

Example

#include <bio/alphabet/cigar/cigar.hpp>
#include <bio/alphabet/cigar/cigar_op.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::cigar letter{10, 'M'_cigar_op};
 
    uint32_t size{get<0>(letter)};                // Note this is equivalent to get<uint32_t>(letter)
    bio::alphabet::cigar_op cigar_char{get<1>(letter)};     // Note this is equivalent to get<bio::alphabet::cigar_op>(letter)
 
    fmt::print("Size is {}\n", size);
    fmt::print("Cigar char is {}\n", cigar_char);
 
}

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

bio/alphabet/cigar/cigar.hpp

Public Member Functions

Friends

Detailed Description

ABI

Example

Member Function Documentation

◆ assign_rank()

Complexity

Exceptions

◆ assign_string()

◆ to_rank()

Complexity

Exceptions

◆ to_string()

Friends And Related Function Documentation

◆ get [1/4]

Example

◆ get [2/4]

Example

◆ get [3/4]

Example

◆ get [4/4]

Example