SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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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.
 

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.
 

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.

Member Function Documentation

◆ char_to_rank()

static constexpr rank_type seqan3::dna16sam::char_to_rank ( char_type const  chr)
inlinestaticconstexprprivate

Returns the rank representation of character.

This function is required by seqan3::alphabet_base.

◆ rank_complement()

static constexpr rank_type seqan3::dna16sam::rank_complement ( rank_type const  rank)
inlinestaticconstexprprivate

Returns the complement by rank.

This function is required by seqan3::nucleotide_base.

◆ rank_to_char()

static constexpr char_type seqan3::dna16sam::rank_to_char ( rank_type const  rank)
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).

Friends And Related Symbol Documentation

◆ dna16sam_vector

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

This entity is stable. Since version 3.1.

◆ operator""_dna16sam() [1/2]

constexpr dna16sam_vector operator""_dna16sam ( char const *  s,
size_t  n 
)
related

The seqan3::dna16sam string literal.

Returns
seqan3::dna16sam_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::dna16sam_vector:

// 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
// generated from test/snippet/alphabet/nucleotide/@target_alphabet@_literal.cpp.in
int main()
{
using namespace seqan3::literals;
seqan3::dna16sam_vector sequence1{"ACGTTA"_dna16sam};
seqan3::dna16sam_vector sequence2 = "ACGTTA"_dna16sam;
auto sequence3 = "ACGTTA"_dna16sam;
}

This entity is stable. Since version 3.1.

◆ operator""_dna16sam() [2/2]

constexpr dna16sam operator""_dna16sam ( char const  c)
related

The seqan3::dna16sam char literal.

Returns
seqan3::dna16sam
Parameters
[in]cThe character to assign from.

You can use this char literal to assign a seqan3::dna16sam character:

// 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
// generated from test/snippet/alphabet/nucleotide/@target_alphabet@_char_literal.cpp.in
int main()
{
using namespace seqan3::literals;
seqan3::dna16sam letter1{'A'_dna16sam};
auto letter2 = 'A'_dna16sam;
}

This entity is stable. Since version 3.1.

Member Data Documentation

◆ char_to_rank_table

constexpr std::array<rank_type, 256> seqan3::dna16sam::char_to_rank_table
staticconstexprprivate
Initial value:
{
[]() constexpr {
ret.fill(15u);
for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
{
ret[rank_to_char_table[rnk]] = rnk;
ret[to_lower(rank_to_char_table[rnk])] = rnk;
}
ret['U'] = ret['T'];
ret['u'] = ret['t'];
return ret;
}()
}
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.
Definition alphabet_base.hpp:196
static constexpr char_type rank_to_char_table[alphabet_size]
The lookup table used in rank_to_char.
Definition dna16sam.hpp:74
T fill(T... args)
constexpr char_type to_lower(char_type const c) noexcept
Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
Definition transform.hpp:80

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.

static constexpr char_type rank_to_char(rank_type const rank)
{
// not possible because of static not being allowed within a constexpr function
static constexpr lookup_table = ...;
return lookup_table[rank];
}
static constexpr char_type rank_to_char(rank_type const rank)
{
// up-to the compiler to optimise, no guarantee that a lookup table is used.
constexpr lookup_table = ...;
return lookup_table[rank];
}
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition alphabet_base.hpp:77
std::conditional_t< std::same_as< char_t, void >, char, char_t > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition alphabet_base.hpp:69
rank_type rank
The value of the alphabet letter is stored as the rank.
Definition alphabet_base.hpp:258
static constexpr char_type rank_to_char(rank_type const rank)
Returns the character representation of rank.
Definition dna16sam.hpp:106
See also
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99320 for the progress on gcc

◆ rank_complement_table

constexpr rank_type seqan3::dna16sam::rank_complement_table[alphabet_size]
staticconstexprprivate
Initial value:
{
15,
8,
4,
12,
2,
10,
6,
14,
1,
9,
5,
13,
3,
11,
7,
15
}

The rank complement table.

◆ rank_to_char_table

constexpr char_type seqan3::dna16sam::rank_to_char_table[alphabet_size] {'=', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'}
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.

static constexpr char_type rank_to_char(rank_type const rank)
{
// not possible because of static not being allowed within a constexpr function
static constexpr lookup_table = ...;
return lookup_table[rank];
}
static constexpr char_type rank_to_char(rank_type const rank)
{
// up-to the compiler to optimise, no guarantee that a lookup table is used.
constexpr lookup_table = ...;
return lookup_table[rank];
}
See also
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99320 for the progress on gcc

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