SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
Loading...
Searching...
No Matches
seqan3::dna16sam Class Reference

A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('='). More...

#include <seqan3/alphabet/nucleotide/dna16sam.hpp>

+ Inheritance diagram for seqan3::dna16sam:

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 dna16samoperator= (dna16sam const &) noexcept=default
 Defaulted.
 
constexpr dna16samoperator= (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_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (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.
 

Related Symbols

(Note that these are not member symbols.)

using dna16sam_vector = std::vector< dna16sam >
 Alias for a std::vector of seqan3::dna16sam.
 

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()).
 

Detailed Description

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'.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
int main()
{
using namespace seqan3::literals;
seqan3::dna16sam letter{'A'_dna16sam};
letter.assign_char('=');
seqan3::debug_stream << letter << '\n'; // prints "="
letter.assign_char('F'); // Unknown characters are implicitly converted to N.
seqan3::debug_stream << letter << '\n'; // "N";
}
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=').
Definition dna16sam.hpp:45
Provides seqan3::debug_stream and related types.
Provides seqan3::dna16sam.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
The SeqAn namespace for literals.

This entity is stable. Since version 3.1.

Friends And Related Symbol Documentation

◆ dna16sam_vector

Alias for a std::vector of seqan3::dna16sam.

This entity is stable. Since version 3.1.


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