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
	Defaulted.
	method_local (method_local const &)=default
	Defaulted.
	method_local (method_local &&)=default
	Defaulted.
method_local &	operator= (method_local const &)=default
	Defaulted.
method_local &	operator= (method_local &&)=default
	Defaulted.
	~method_local ()=default
	Defaulted.

Detailed Descriptionno-api

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.

Example

#include <seqan3/alignment/configuration/align_config_method.hpp>
#include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
 
using namespace seqan3::literals;
 
int main()
{
    auto min_cfg = seqan3::align_cfg::method_local{} |
                   seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
                                                                                       seqan3::mismatch_score{-5}}};
 
    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';
}

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

• seqan3/alignment/configuration/align_config_method.hpp