SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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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. | |
Public Member Functions inherited from seqan3::nucleotide_base< dna3bs, 3 > | |
constexpr dna3bs | 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< dna3bs, 3 > |
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', 'G', 'T'} |
The lookup table used in rank_to_char. | |
Related Symbols | |
(Note that these are not member symbols.) | |
using | dna3bs_vector = std::vector< dna3bs > |
Alias for a std::vector of seqan3::dna3bs. | |
Nucleotide literals | |
constexpr dna3bs | operator""_dna3bs (char const c) noexcept |
The seqan3::dna3bs char literal. | |
constexpr dna3bs_vector | operator""_dna3bs (char const *s, std::size_t n) |
The seqan3::dna3bs 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< dna3bs, 3 > | |
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()). | |
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 seqan3::dna3bs sequence will further reduce the alphabet to only 'T' and 'A', thereby losing all information about 'G'. When working with bisulfite data, we recommend to create the reverse complement of the seqan3::dna4 / seqan3::dna5 / seqan3::dna15 range first and convert to seqan3::dna3bs later. This avoids simplifying the data by automatically setting 'A' as the complement of 'C'. As an example: The sequence 'ACGTGC' in seqan3::dna4 would be 'ATGTGT' in seqan3::dna3bs. The complement of this seqan3::dna3bs sequence would be 'TATATA', however when complementing the seqan3::dna4 sequence first and afterwards transforming it into seqan3::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 'A'_dna3bs or use the function seqan3::dna3bs::assign_char().
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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.
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related |
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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.
You can use this char literal to assign a seqan3::dna3bs 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.