The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=. More...
#include <seqan3/alphabet/cigar/cigar_op.hpp>
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | cigar_op () noexcept=default |
Defaulted. | |
constexpr | cigar_op (cigar_op const &) noexcept=default |
Defaulted. | |
constexpr | cigar_op (cigar_op &&) noexcept=default |
Defaulted. | |
constexpr cigar_op & | operator= (cigar_op const &) noexcept=default |
Defaulted. | |
constexpr cigar_op & | operator= (cigar_op &&) noexcept=default |
Defaulted. | |
~cigar_op () 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 cigar_op & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr cigar_op & | 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< 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 Functions | |
(Note that these are not member functions.) | |
Literals | |
cigar_op | operator""_cigar_op (char const c) noexcept |
The seqan3::cigar_op char literal. More... | |
Requirements for std::totally_ordered | |
You can expect these functions on all types that implement std::totally_ordered. | |
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::equality_comparable | |
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... | |
The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=.
The CIGAR string can be either basic or extended. The only difference in the extended cigar alphabet is that aligned bases are classified as an actual match ('=') or mismatch ('X'). In contrast, the basic cigar alphabet only indicated the aligned status with an 'M', without further information if the bases are actually equal or not.
The main purpose of the seqan3::cigar_op alphabet is to be used in the seqan3::cigar composition, where a cigar operation is paired with a count value.
Example usage:
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defaultnoexcept |
Defaulted.
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inlineconstexprnoexceptinherited |
Assign from a character, implicitly converts invalid characters.
c | The character to be assigned. |
Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Assign from a numeric value.
c | The rank to be assigned. |
Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Return the letter as a character of char_type.
Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
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related |
The seqan3::cigar_op char literal.