seqan3::align_cfg::scoring< scoring_scheme_t > Struct Template Reference

Sets the scoring scheme for the alignment algorithm. More...

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

Inheritance diagram for seqan3::align_cfg::scoring< scoring_scheme_t >:

Public Attributes
scoring_scheme_t	value
	The stored config value.

Related Functions
(Note that these are not member functions.)
Type deduction guides
template<typename scheme_t >
	scoring (scheme_t) -> scoring< remove_cvref_t< scheme_t >>
	Deduces the scoring scheme type from the constructor argument.

Detailed Description

template<typename scoring_scheme_t>
struct seqan3::align_cfg::scoring< scoring_scheme_t >

Sets the scoring scheme for the alignment algorithm.

Template Parameters

scoring_scheme_t

The type of the scoring scheme. Must satisfy seqan3::ScoringScheme.

The scoring scheme allows to specify how two symbols of an alphabet are scored inside of the alignment algorithm. The scheme depends on the alphabet type of the passed sequences and must be chosen accordingly. During the configuration of the pairwise alignment algorithm a static assert is triggered if the scoring scheme is not compatible with the given alphabet types. Accordingly, this configuration cannot be defaulted since it depends on the sequences and must be given as a minimal configuration.

Example

#include <seqan3/alignment/configuration/align_config_mode.hpp>
#include <seqan3/alignment/configuration/align_config_scoring.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;

int main()
{
    auto min_cfg = align_cfg::mode{global_alignment} |
                   align_cfg::scoring{nucleotide_scoring_scheme{match_score{4}, mismatch_score{-5}}};

    auto seq1 = "ACGT"_dna4;
    auto seq2 = "ACCT"_dna4;
    for (auto res : align_pairwise(std::tie(seq1, seq2), min_cfg))
        debug_stream << res.score() << '\n';
}

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

• seqan3/alignment/configuration/align_config_scoring.hpp