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

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, this configuration must be provided for the alignment algorithm and cannot be defaulted.

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 seqan3::operator""_dna4;
 
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';
}

Constructor & Destructor Documentation

~method_local()

seqan3::align_cfg::method_local::~method_local ( )

default

Defaulted.

---

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

• seqan3/alignment/configuration/align_config_method.hpp