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. | |
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constexpr sam_dna16 | complement () const noexcept |
Return the complement of the letter. More... | |
constexpr | nucleotide_base (other_nucl_type const &other) noexcept |
Allow explicit construction from any other nucleotide type and convert via the character representation. | |
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constexpr | alphabet_base () noexcept=default |
Defaulted. | |
constexpr | alphabet_base (alphabet_base const &) noexcept=default |
Defaulted. | |
constexpr | alphabet_base (alphabet_base &&) noexcept=default |
Defaulted. | |
constexpr alphabet_base & | operator= (alphabet_base const &) noexcept=default |
Defaulted. | |
constexpr alphabet_base & | operator= (alphabet_base &&) noexcept=default |
Defaulted. | |
~alphabet_base () noexcept=default | |
Defaulted. | |
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... | |
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... | |
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... | |
Additional Inherited Members | |
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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... | |
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static constexpr detail::min_viable_uint_t< size > | alphabet_size = size |
The size of the alphabet, i.e. the number of different values it can take. More... | |
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using | char_type = std::conditional_t< std::same_as< char_t, void >, char, char_t > |
The char representation; conditional needed to make semi alphabet definitions legal. More... | |
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()). 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'.
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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:
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related |
The seqan3::sam_dna16 char literal.
[in] | c | The character to assign from. |