The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)). More...
#include <seqan3/alphabet/nucleotide/dna3bs.hpp>
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | dna3bs () noexcept=default |
Defaulted. | |
constexpr | dna3bs (dna3bs const &) noexcept=default |
Defaulted. | |
constexpr | dna3bs (dna3bs &&) noexcept=default |
Defaulted. | |
constexpr dna3bs & | operator= (dna3bs const &) noexcept=default |
Defaulted. | |
constexpr dna3bs & | operator= (dna3bs &&) noexcept=default |
Defaulted. | |
~dna3bs () noexcept=default | |
Defaulted. | |
Read functions | |
constexpr dna3bs | 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 dna3bs & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr dna3bs & | 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 | dna3bs_vector = std::vector< dna3bs > |
Alias for an std::vector of seqan3::dna3bs. | |
Literals | |
constexpr dna3bs | operator""_dna3bs (char const c) noexcept |
The seqan3::dna3bs char literal. More... | |
dna3bs_vector | operator""_dna3bs (char const *s, std::size_t n) |
The seqan3::dna3bs string literal. More... | |
The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)).
This alphabet represents a reduced version that can be used when dealing with bisulfite-converted data. All 'C's are converted to a 'T' in order to allow comparison of normal sequences with bisulfite-converted sequences. For completeness, this nucleotide alphabet has a complement table, however, it is not recommended to use it when dealing with bisulfite data because the complement of T is ambiguous in reads from bisulfite sequencing. A 'T' can represent a true thymidine or an unmethylated 'C' that was converted into a 'T'. Therefore, complementing a dna4bs sequence will further reduce the alphabet to only 'T' and 'A', thereby loosing all information about 'G'. When working with bisulfite data, we recommend to create the reverse complement of the dna4/5/15 range first and convert to dna3bs later. This avoids simplifying the data by automatically setting 'A' as the complement of 'C'. As an example: The sequence 'ACGTGC' in dna4 would be 'ATGTGT' in dna3bs. The complement of this dna3bs sequence would be 'TATATA', however when complementing the dna4 sequence first and afterwards transforming it into dna3bs, it would be 'TGTATG' which preserves more information from the original sequence.
Like most alphabets, this alphabet cannot be initialised directly from its character representation. Instead initialise/assign from the character literal or use the function seqan3::dna3bs::assign_char().
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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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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.
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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.
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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::dna3bs string literal.
You can use this string literal to easily assign to dna3bs_vector:
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related |
The seqan3::dna3bs char literal.