The cigar alphabet 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 (indirect_component_type const alph) noexcept
	Construction via a value of a subtype that is assignable to one of the components. More...

constexpr cigar &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components. More...

constexpr cigar &	operator= (indirect_component_type const alph) noexcept
	Assignment via a value of a subtype that is assignable to one of the components. More...

Read functions
small_string< 11 >	to_char () const noexcept
	Return the character representation.

Write functions
cigar &	assign_char (small_string< 11 > const s) noexcept
	Assign from the character representation.

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.

Comparison operators (against indirect component_list)
`*this` is cast to the component type before comparison. (These overloads enable comparison for all types that a component type is comparable with).
constexpr bool	operator== (indirect_component_type const rhs) const noexcept

constexpr bool	operator!= (indirect_component_type const rhs) const noexcept

constexpr bool	operator< (indirect_component_type const rhs) const noexcept

constexpr bool	operator> (indirect_component_type const rhs) const noexcept

constexpr bool	operator<= (indirect_component_type const rhs) const noexcept

constexpr bool	operator>= (indirect_component_type const rhs) const noexcept

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

Write functions
constexpr derived_type &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...

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

Static Public Attributes
static detail::min_viable_uint_t< size > constexpr	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< 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()).

Related Functions
(Note that these are not member functions.)
Requirements for std::StrictTotallyOrdered
You can expect these functions on all types that implement std::StrictTotallyOrdered.
bool	operator< (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator<= (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator> (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator>= (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

Requirements for std::EqualityComparable
You can expect these functions on all types that implement std::Equality_comparable.
bool	operator== (type const &lhs, type const &rhs)
	(In-)Equality comparison. More...

bool	operator!= (type const &lhs, type const &rhs)
	(In-)Equality comparison. More...

Requirements for std::Swappable
You can expect these functions on all types that implement std::Swappable.
void	swap (t &lhs, t &rhs)
	Swaps the contents of two objects. More...

Comparison operators
Free function (in-)equality comparison operators that forward to member operators (for types != self).
constexpr bool	operator== (indirect_component_type const lhs, alphabet_tuple_base< cigar, component_types... > const rhs) noexcept

constexpr bool	operator!= (indirect_component_type const lhs, alphabet_tuple_base< cigar, indirect_component_types... > const rhs) noexcept

constexpr bool	operator< (indirect_component_type const lhs, alphabet_tuple_base< cigar, indirect_component_types... > const rhs) noexcept

constexpr bool	operator> (indirect_component_type const lhs, alphabet_tuple_base< cigar, indirect_component_types... > const rhs) noexcept

constexpr bool	operator<= (indirect_component_type const lhs, alphabet_tuple_base< cigar, indirect_component_types... > const rhs) noexcept

constexpr bool	operator>= (indirect_component_type const lhs, alphabet_tuple_base< cigar, indirect_component_types... > const rhs) noexcept

Detailed Description

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

This alphabet 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.

The "char representation" of this alphabet is a seqan3::small_string. This has some implications when using it in code that doesn't expect a range of symbols.

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 << std::endl; // "13M"
    seqan3::assign_char_to("14X", c);
    seqan3::debug_stream << c << std::endl; // "14X"
}

Constructor & Destructor Documentation

◆ cigar() [1/2]

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

inlinenoexcept

Construction via a value of one of the components.

Template Parameters

component_type Must be one uniquely contained in the type list of the composite.

Parameters

alph	The value of a component that should be assigned.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

qualified<dna4, phred42> letter1{'C'_dna4}; // creates {'C'_dna4, phred42{0}}

qualified<dna4, phred42> letter2{phred42{1}}; // creates {'A'_dna4, phred42{1}}

◆ cigar() [2/2]

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

inlinenoexcept

Construction via a value of a subtype that is assignable to one of the components.

Template Parameters

indirect_component_type Type that models seqan3::WeaklyAssignable for one of the component types.

Parameters

alph	The value that should be assigned.

Note that the value will be assigned to the FIRST type T that fulfils Assignable<T, indirect_component_type>, regardless if other types are also fit for assignment.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

// The following creates {'C'_dna4, phre42{0}}
qualified<dna4, phred42> letter1{'C'_dna4};
// The following also creates {'C'_dna4, phred42{0}}, since rna4 assignable to dna4
qualified<dna4, phred42> letter2{'C'_rna4};
if (letter1 == letter2)
    debug_stream << "yeah\n"; // yeah

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 c )

inlinenoexceptinherited

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()

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 )

inlinenoexceptinherited

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.

◆ operator=() [1/2]

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

inlinenoexcept

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

alph	The value of a component that should be assigned.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

qualified<dna4, phred42> letter1{'T'_dna4, phred42{1}};
letter1 = 'C'_dna4; // yields {'C'_dna4, phred42{1}}
letter1 = phred42{2}; // yields {'C'_dna4, phred42{2}}

◆ operator=() [2/2]

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

inlinenoexcept

Assignment via a value of a subtype that is assignable to one of the components.

Template Parameters

indirect_component_type Type that models seqan3::WeaklyAssignable for one of the component types.

Parameters

alph	The value of a component that should be assigned.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

qualified<dna4, phred42> letter1{'T'_dna4, phred42{1}};
letter1 = 'C'_rna4; // yields {'C'_dna4, phred42{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

inlinenoexceptinherited

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.

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

seqan3/alphabet/cigar/cigar.hpp

Public Member Functions

Static Public Attributes

Protected Types

Related Functions

Detailed Description

Example

Constructor & Destructor Documentation

◆ cigar() [1/2]

◆ cigar() [2/2]

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_rank()

Complexity

Exceptions

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ to_rank()

Complexity

Exceptions