SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::align_cfg::method_local Class Reference

Sets the local alignment method. More...

#include <seqan3/alignment/configuration/align_config_method.hpp>

+ Inheritance diagram for seqan3::align_cfg::method_local:

Public Member Functions

Constructors, destructor and assignment
 method_local ()=default
 method_local (method_local const &)=default
 method_local (method_local &&)=default
method_localoperator= (method_local const &)=default
method_localoperator= (method_local &&)=default
 ~method_local ()=default

Detailed Description

Sets the local alignment method.

The alignment algorithm can be categorised in different methods. For example, the local and the global alignment are two different methods, while the semi-global alignment is a variation of the global alignment. This differentiation makes it possible to define a subset of configurations that can work with a particular method. Since it is not possible to guess what the desired method for a user is, there is no default and this configuration must always be provided for the alignment algorithm.


using seqan3::operator""_dna4;
int main()
auto seq1 = "TCGT"_dna4;
auto seq2 = "ACGA"_dna4;
for (auto res : align_pairwise(std::tie(seq1, seq2), min_cfg))
seqan3::debug_stream << res.score() << '\n';
Provides global and local alignment configurations.
Provides seqan3::align_cfg::scoring_scheme.
Provides pairwise alignment function.
Sets the local alignment method.
Definition: align_config_method.hpp:43
A data structure for managing and computing the score of two nucleotides.
Definition: nucleotide_scoring_scheme.hpp:38
Provides seqan3::debug_stream and related types.
Provides seqan3::dna4, container aliases and string literals.
constexpr auto align_pairwise(sequence_t &&seq, alignment_config_t const &config)
Computes the pairwise alignment for a pair of sequences or a range over sequence pairs.
Definition: align_pairwise.hpp:137
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
Provides seqan3::nucleotide_scoring_scheme.
Sets the scoring scheme for the alignment algorithm.
Definition: align_config_scoring_scheme.hpp:45
A strong type of underlying type score_type that represents the score of two matching characters.
Definition: scoring_scheme_base.hpp:41
A strong type of underlying type score_type that represents the score two different characters.
Definition: scoring_scheme_base.hpp:66
T tie(T... args)

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