seqan3::cigar Class Reference

The cigar semialphabet pairs a counter with a seqan3::cigar_op letter. More...

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

Inheritance diagram for seqan3::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 (component_type const alph) noexcept
	Construction via a value of one of the components. More...
constexpr cigar &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components. More...
Read functions
small_string< 11 >	to_string () const noexcept
	Return the string representation.
Write functions
cigar &	assign_string (small_string< 11 > const s) noexcept
	Assign from the string representation.
Get functions
template<size_t index>
constexpr auto	get (cigar &l) noexcept
	Tuple-like access to the contained components. More...
template<typename type >
constexpr auto	get (cigar &l) noexcept
	Tuple-like access to the contained components. More...
Read functions
All read operations are constant complexity.
constexpr	operator type () const noexcept
	Implicit cast to a single letter. Works only if the type is unique in the type list.
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 cigar &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...
constexpr cigar &	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.

Protected Types
Member types
using	char_type = std::conditional_t< std::same_as< void, void >, char, void >
	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()).

Detailed Description

The cigar semialphabet pairs a counter with a seqan3::cigar_op letter.

This semialphabet represents a unit in a CIGAR string, typically found in the SAM and BAM formats. It consists of a number and a seqan3::cigar_op symbol.

It has a "visual representation", but since this is a string and not a char, the type only models seqan3::writable_semialphabet and not seqan3::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 seqan3::cigar_op.

Example

#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream.hpp>
 
using seqan3::operator""_cigar_op;
 
int main()
{
    seqan3::cigar c{13, 'M'_cigar_op};
    seqan3::debug_stream << c << '\n'; // "13M"
 
    c.assign_string("14X");
    seqan3::debug_stream << c << '\n'; // "14X"
}

Constructor & Destructor Documentation

cigar()

constexpr seqan3::cigar::cigar ( component_type const  alph )

inlineconstexprnoexcept

Construction via a value of one of the components.

Template Parameters

component_type

One of the component types; must be uniquely contained in the type list of the composite.

Parameters

[in]

alph

The value of a component that should be assigned.

#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/alphabet/cigar/cigar_op.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_cigar_op;
 
    seqan3::cigar letter1{0};
    // creates 0M, as the cigar_op field is not provided.
    seqan3::cigar letter2{'M'_cigar_op};
    // creates 0M, as the integer field is not provided.
 
    if (letter1 == letter2)
        seqan3::debug_stream << "yeah\n"; // yeah
 
    seqan3::cigar letter3{10, 'I'_cigar_op};
    // creates 10I, as both fields are explicitly given.
}

Member Function Documentation

assign_char()

constexpr cigar & seqan3::alphabet_base< cigar , size, void >::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.

assign_rank()

constexpr cigar & seqan3::alphabet_base< cigar , size, void >::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.

get() [1/2]

template<size_t index>

constexpr auto seqan3::cigar::get ( cigar &  l )

inlineconstexprnoexcept

Tuple-like access to the contained components.

Template Parameters

index

Return the i-th element.

Returns

A proxy to the contained element that models the same alphabets concepts and supports assignment.

#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/alphabet/cigar/cigar_op.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::get;
    using seqan3::operator""_cigar_op;
 
    seqan3::cigar letter{10, 'M'_cigar_op};
 
    uint32_t size{get<0>(letter)};               // Note this is equivalent to get<uint32_t>(letter)
    seqan3::cigar_op cigar_char{get<1>(letter)}; // Note this is equivalent to get<seqan3::cigar_op>(letter)
 
    seqan3::debug_stream << "Size is "       << size       << '\n';
    seqan3::debug_stream << "Cigar char is " << cigar_char << '\n'; // seqan3::debug_stream converts to char on the fly.
 
}

get() [2/2]

template<typename type >

constexpr auto seqan3::cigar::get ( cigar &  l )

inlineconstexprnoexcept

Tuple-like access to the contained components.

Template Parameters

type	Return the element of specified type; only available if the type is unique in the set of components.

Returns

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

#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/alphabet/cigar/cigar_op.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::get;
    using seqan3::operator""_cigar_op;
 
    seqan3::cigar letter{10, 'M'_cigar_op};
 
    uint32_t size{get<uint32_t>(letter)};                       // Note this is equivalent to get<0>(letter)
    seqan3::cigar_op cigar_char{get<seqan3::cigar_op>(letter)}; // Note this is equivalent to get<1>(letter)
 
    seqan3::debug_stream << "Size is "       << size       << '\n';
    seqan3::debug_stream << "Cigar char is " << cigar_char << '\n'; // seqan3::debug_stream converts to char on the fly.
 
}

operator=()

constexpr cigar& seqan3::cigar::operator= ( component_type const  alph )

inlineconstexprnoexcept

Assignment via a value of one of the components.

Template Parameters

component_type

One of the component types; must be uniquely contained in the type list of the composite.

Parameters

[in]

alph

The value of a component that should be assigned.

#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/alphabet/cigar/cigar_op.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_cigar_op;
 
    seqan3::cigar letter{10, 'I'_cigar_op};
 
    letter = 'D'_cigar_op;  // yields 10D
    letter = 20; // yields 20D
 
    if (letter == seqan3::cigar{20, 'D'_cigar_op})
        seqan3::debug_stream << "yeah\n";
}

to_char()

constexpr char_type seqan3::alphabet_base< cigar , size, void >::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.

to_rank()

constexpr rank_type seqan3::alphabet_base< cigar , size, void >::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.

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

• seqan3/alphabet/cigar/cigar.hpp