A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('='). More...
#include <seqan3/alphabet/nucleotide/sam_dna16.hpp>
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | sam_dna16 () noexcept=default |
Defaulted. | |
constexpr | sam_dna16 (sam_dna16 const &) noexcept=default |
Defaulted. | |
constexpr | sam_dna16 (sam_dna16 &&) noexcept=default |
Defaulted. | |
constexpr sam_dna16 & | operator= (sam_dna16 const &) noexcept=default |
Defaulted. | |
constexpr sam_dna16 & | operator= (sam_dna16 &&) noexcept=default |
Defaulted. | |
~sam_dna16 () noexcept=default | |
Defaulted. | |
Read functions | |
constexpr sam_dna16 | complement () const noexcept |
Return the complement of the letter. More... | |
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 sam_dna16 & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr sam_dna16 & | assign_rank (rank_type const c) noexcept |
Assign from a numeric value. More... | |
Static Public Member Functions | |
static constexpr bool | char_is_valid (char_type const c) noexcept |
Validate whether a character value has a one-to-one mapping to an alphabet 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.) | |
using | sam_dna16_vector = std::vector< sam_dna16 > |
Alias for an std::vector of seqan3::sam_dna16. | |
Literals | |
constexpr sam_dna16 | operator""_sam_dna16 (char const c) noexcept |
The seqan3::sam_dna16 char literal. More... | |
sam_dna16_vector | operator""_sam_dna16 (char const *s, size_t n) |
The seqan3::sam_dna16 string 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... | |
A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=').
The seqan3::sam_dna16 alphabet is the nucleotide alphabet used inside the SAM, BAM and CRAM formats. It has all the letters of the seqan3::dna15 alphabet and the extra alphabet character '=' which denotes a nucleotide character identical to the reference. Without the context of this reference sequence, no assumptions can be made about the actual value of '=' letter.
Note that you can assign 'U' as a character to sam_dna16 and it will silently be converted to 'T'. Lower case letters are accepted when assigning from char (just like seqan3::dna15) and unknown characters are silently converted to 'N'.
The complement is the same as for seqan3::dna15, with the addition that the complement of '=' is unknown and therefore set to 'N'.
|
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.
|
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.
|
inlinestaticconstexprnoexceptinherited |
Validate whether a character value has a one-to-one mapping to an alphabet value.
Satisfies the seqan3::semialphabet::char_is_valid_for() requirement via the seqan3::char_is_valid_for() wrapper.
Behaviour specific to nucleotides: True also for lower case letters that silently convert to their upper case and true also for U/T respectively, e.g. 'U' is a valid character for seqan3::dna4, because its informational content is identical to 'T'.
Constant.
Guaranteed not to throw.
|
inlineconstexprnoexceptinherited |
Return the complement of the letter.
See Nucleotide for the actual values.
Provides an implementation for seqan3::complement, required to model seqan3::nucleotide_alphabet.
Constant.
Guaranteed not to throw.
|
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.
|
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.
|
related |
The seqan3::sam_dna16 string literal.
[in] | s | The string literal to assign from. |
[in] | n | The length of the string literal s. |
You can use this string literal to easily assign to seqan3::sam_dna16_vector:
|
related |
The seqan3::sam_dna16 char literal.
[in] | c | The character to assign from. |