libseqan3-dev/html/aliases_8hpp_source.html

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin

// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik

// SPDX-License-Identifier: BSD-3-Clause


#pragma once


#include <seqan3/alphabet/concept.hpp>

#include <seqan3/alphabet/nucleotide/dna15.hpp>

#include <seqan3/alphabet/nucleotide/dna4.hpp>

#include <seqan3/alphabet/nucleotide/dna5.hpp>

#include <seqan3/alphabet/nucleotide/rna15.hpp>

#include <seqan3/alphabet/nucleotide/rna4.hpp>

#include <seqan3/alphabet/nucleotide/rna5.hpp>

#include <seqan3/alphabet/quality/concept.hpp>

#include <seqan3/alphabet/quality/phred42.hpp>

#include <seqan3/alphabet/quality/qualified.hpp>


namespace seqan3

{


using dna4q = qualified<dna4, phred42>;


using dna5q = qualified<dna5, phred42>;


using rna4q = qualified<rna4, phred42>;


using rna5q = qualified<rna5, phred42>;


using dna15q = qualified<dna15, phred42>;


using rna15q = qualified<rna15, phred42>;


} // namespace seqan3

concept.hpp
Core alphabet concept and free function/type trait wrappers.

concept.hpp
Quality alphabet concept.

seqan3::qualified
Joins an arbitrary alphabet with a quality alphabet.
Definition qualified.hpp:59

dna15.hpp
Provides seqan3::dna15, container aliases and string literals.

dna4.hpp
Provides seqan3::dna4, container aliases and string literals.

dna5.hpp
Provides seqan3::dna5, container aliases and string literals.

seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26

seqan3::dna15q
qualified< dna15, phred42 > dna15q
An alphabet that stores a seqan3::dna15 letter and an seqan3::qualified letter at each position.
Definition aliases.hpp:59

seqan3::rna4q
qualified< rna4, phred42 > rna4q
An alphabet that stores a seqan3::rna4 letter and an seqan3::phred42 letter at each position.
Definition aliases.hpp:45

seqan3::rna15q
qualified< rna15, phred42 > rna15q
An alphabet that stores a seqan3::rna15 letter and an seqan3::qualified letter at each position.
Definition aliases.hpp:66

seqan3::dna4q
qualified< dna4, phred42 > dna4q
An alphabet that stores a seqan3::dna4 letter and an seqan3::phred42 letter at each position.
Definition aliases.hpp:31

seqan3::dna5q
qualified< dna5, phred42 > dna5q
An alphabet that stores a seqan3::dna5 letter and an seqan3::phred42 letter at each position.
Definition aliases.hpp:38

seqan3::rna5q
qualified< rna5, phred42 > rna5q
An alphabet that stores a seqan3::rna5 letter and an seqan3::phred42 letter at each position.
Definition aliases.hpp:52

phred42.hpp
Provides seqan3::phred42 quality scores.

qualified.hpp
Provides quality alphabet composites.

rna15.hpp
Provides seqan3::rna15, container aliases and string literals.

rna4.hpp
Provides seqan3::rna4, container aliases and string literals.

rna5.hpp
Provides seqan3::rna5, container aliases and string literals.