SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('='). More...
#include <seqan3/alphabet/nucleotide/dna16sam.hpp>
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | dna16sam () noexcept=default |
Defaulted. | |
constexpr | dna16sam (dna16sam const &) noexcept=default |
Defaulted. | |
constexpr | dna16sam (dna16sam &&) noexcept=default |
Defaulted. | |
constexpr dna16sam & | operator= (dna16sam const &) noexcept=default |
Defaulted. | |
constexpr dna16sam & | operator= (dna16sam &&) noexcept=default |
Defaulted. | |
~dna16sam () noexcept=default | |
Defaulted. | |
Public Member Functions inherited from seqan3::nucleotide_base< dna16sam, 16 > | |
constexpr dna16sam | complement () const noexcept |
Return the complement of the letter. | |
constexpr | nucleotide_base (other_nucl_type const &other) noexcept |
Allow explicit construction from any other nucleotide type and convert via the character representation. | |
Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t > | |
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. | |
constexpr rank_type | to_rank () const noexcept |
Return the letter's numeric value (rank in the alphabet). | |
constexpr derived_type & | assign_char (char_type const chr) noexcept |
Assign from a character, implicitly converts invalid characters. | |
constexpr derived_type & | assign_rank (rank_type const c) noexcept |
Assign from a numeric value. | |
Private Types | |
using | base_t = nucleotide_base< dna16sam, 16 > |
The base class. | |
Static Private Member Functions | |
static constexpr rank_type | char_to_rank (char_type const chr) |
Returns the rank representation of character. | |
static constexpr rank_type | rank_complement (rank_type const rank) |
Returns the complement by rank. | |
static constexpr char_type | rank_to_char (rank_type const rank) |
Returns the character representation of rank. | |
Private Attributes | |
friend | base_t |
Befriend seqan3::nucleotide_base. | |
Static Private Attributes | |
static constexpr std::array< rank_type, 256 > | char_to_rank_table |
The lookup table used in char_to_rank. | |
static constexpr rank_type | rank_complement_table [alphabet_size] |
The rank complement table. | |
static constexpr char_type | rank_to_char_table [alphabet_size] {'=', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'} |
The lookup table used in rank_to_char. | |
Related Symbols | |
(Note that these are not member symbols.) | |
using | dna16sam_vector = std::vector< dna16sam > |
Alias for a std::vector of seqan3::dna16sam. | |
Nucleotide literals | |
constexpr dna16sam | operator""_dna16sam (char const c) noexcept |
The seqan3::dna16sam char literal. | |
constexpr dna16sam_vector | operator""_dna16sam (char const *s, size_t n) |
The seqan3::dna16sam string literal. | |
Related Symbols inherited from semialphabet | |
template<cereal_output_archive archive_t, semialphabet alphabet_t> | |
alphabet_rank_t< alphabet_t > | save_minimal (archive_t const &, alphabet_t const &l) |
Save an alphabet letter to stream. | |
template<cereal_input_archive archive_t, typename wrapped_alphabet_t > | |
void | load_minimal (archive_t const &, wrapped_alphabet_t &&l, alphabet_rank_t< detail::strip_cereal_wrapper_t< wrapped_alphabet_t > > const &r) |
Restore an alphabet letter from a saved rank. | |
Additional Inherited Members | |
Static Public Member Functions inherited from seqan3::nucleotide_base< dna16sam, 16 > | |
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. | |
Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t > | |
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. | |
Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t > | |
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. | |
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()). | |
A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=').
The seqan3::dna16sam 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 dna16sam 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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inlinestaticconstexprprivate |
Returns the rank representation of character.
This function is required by seqan3::alphabet_base.
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inlinestaticconstexprprivate |
Returns the complement by rank.
This function is required by seqan3::nucleotide_base.
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inlinestaticconstexprprivate |
Returns the character representation of rank.
This function is required by seqan3::alphabet_base.
The representation is the same as in the SAM specifications (which is NOT in alphabetical order).
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related |
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The seqan3::dna16sam 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::dna16sam_vector:
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related |
The seqan3::dna16sam char literal.
[in] | c | The character to assign from. |
You can use this char literal to assign a seqan3::dna16sam character:
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staticconstexprprivate |
The lookup table used in char_to_rank.
We would have defined these lookup tables directly within their respective constexpr functions, but at the time of writing this, gcc did not (clang >= 4 did!) auto-generate lookup tables.
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staticconstexprprivate |
The rank complement table.
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staticconstexprprivate |
The lookup table used in rank_to_char.
We would have defined these lookup tables directly within their respective constexpr functions, but at the time of writing this, gcc did not (clang >= 4 did!) auto-generate lookup tables.