SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
aliases.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
4 // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5 // shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
6 // -----------------------------------------------------------------------------------------------------
7 
13 #pragma once
14 
15 #include <seqan3/alphabet/concept.hpp>
16 #include <seqan3/alphabet/quality/concept.hpp>
17 #include <seqan3/alphabet/quality/phred42.hpp>
18 #include <seqan3/alphabet/quality/qualified.hpp>
19 #include <seqan3/alphabet/nucleotide/dna4.hpp>
20 #include <seqan3/alphabet/nucleotide/dna5.hpp>
21 #include <seqan3/alphabet/nucleotide/dna15.hpp>
22 #include <seqan3/alphabet/nucleotide/rna4.hpp>
23 #include <seqan3/alphabet/nucleotide/rna5.hpp>
24 #include <seqan3/alphabet/nucleotide/rna15.hpp>
25 
26 namespace seqan3
27 {
28 
34 using dna4q = qualified<dna4, phred42>;
35 
41 using dna5q = qualified<dna5, phred42>;
42 
48 using rna4q = qualified<rna4, phred42>;
49 
55 using rna5q = qualified<rna5, phred42>;
56 
62 using dna15q = qualified<dna15, phred42>;
63 
69 using rna15q = qualified<rna15, phred42>;
70 
71 } // 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:61
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:29
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.