SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::sam_dna16 Class Reference

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>

+ Inheritance diagram for seqan3::sam_dna16:

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_dna16operator= (sam_dna16 const &) noexcept=default
 Defaulted.
 
constexpr sam_dna16operator= (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_dna16assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr sam_dna16assign_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 detail::min_viable_uint_t< size > constexpr alphabet_size
 The size of the alphabet, i.e. the number of different values it can take.
 

Protected Types

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()).
 

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. More...
 
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...
 

Detailed Description

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'.

int main()
{
using seqan3::operator""_sam_dna16;
seqan3::sam_dna16 my_letter{'A'_sam_dna16};
my_letter.assign_char('=');
my_letter.assign_char('F'); // unknown characters are implicitly converted to N.
seqan3::debug_stream << my_letter << std::endl; // "N";
}

Member Function Documentation

◆ assign_char()

constexpr sam_dna16 & seqan3::alphabet_base< sam_dna16 , size, char >::assign_char ( char_type const  c)
inlinenoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters
cThe character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

constexpr sam_dna16 & seqan3::alphabet_base< sam_dna16 , size, char >::assign_rank ( rank_type const  c)
inlinenoexceptinherited

Assign from a numeric value.

Parameters
cThe rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ char_is_valid()

static constexpr bool seqan3::nucleotide_base< sam_dna16 , size >::char_is_valid ( char_type const  c)
inlinestaticnoexceptinherited

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'.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ complement()

constexpr sam_dna16 seqan3::nucleotide_base< sam_dna16 , size >::complement ( ) const
inlinenoexceptinherited

Return the complement of the letter.

See Nucleotide for the actual values.

Provides an implementation for seqan3::complement, required to model seqan3::nucleotide_alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

constexpr char_type seqan3::alphabet_base< sam_dna16 , size, char >::to_char ( ) const
inlinenoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< sam_dna16 , size, char >::to_rank ( ) const
inlinenoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

Friends And Related Function Documentation

◆ operator""_sam_dna16() [1/2]

constexpr sam_dna16 operator""_sam_dna16 ( char const  c)
related

The seqan3::sam_dna16 char literal.

Returns
seqan3::sam_dna16
Parameters
[in]cThe character to assign from.

◆ operator""_sam_dna16() [2/2]

sam_dna16_vector operator""_sam_dna16 ( char const *  s,
size_t  n 
)
related

The seqan3::sam_dna16 string literal.

Returns
seqan3::sam_dna16_vector
Parameters
[in]sThe string literal to assign from.
[in]nThe length of the string literal s.

You can use this string literal to easily assign to seqan3::sam_dna16_vector:

int main()
{
using seqan3::operator""_sam_dna16;
seqan3::sam_dna16_vector foo{"ACgtTA"_sam_dna16};
seqan3::sam_dna16_vector bar = "ACG==A"_sam_dna16;
auto bax = "A=GTT!"_sam_dna16;
seqan3::debug_stream << foo << "\n" << bar << "\n" << bax << "\n";
}

◆ sam_dna16_vector


The documentation for this class was generated from the following file: