seqan3::align_cfg::scoring_scheme< scoring_scheme_t > Class Template Reference

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

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

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

Public Member Functions
Constructors, destructor and assignment
constexpr	scoring_scheme ()=default
	Defaulted.
constexpr	scoring_scheme (scoring_scheme const &)=default
	Defaulted.
constexpr	scoring_scheme (scoring_scheme &&)=default
	Defaulted.
constexpr scoring_scheme &	operator= (scoring_scheme const &)=default
	Defaulted.
constexpr scoring_scheme &	operator= (scoring_scheme &&)=default
	Defaulted.
	~scoring_scheme ()=default
	Defaulted.
constexpr	scoring_scheme (scoring_scheme_t scheme)
	Initialises the scoring scheme config with the given scheme.

Public Attributes
scoring_scheme_t	scheme {}
	The scoring scheme to be used in the alignment algorithm.

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

Detailed Description

template<std::semiregular scoring_scheme_t>
class seqan3::align_cfg::scoring_scheme< scoring_scheme_t >

Sets the scoring scheme for the alignment algorithm.

Template Parameters

scoring_scheme_t

The type of the scoring scheme; must model std::semiregular.

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 (see seqan3::scoring_scheme_for). Accordingly, there is no default for this configuration since it depends on the sequences and it must be given as a minimal configuration.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#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_global{}
                 | seqan3::align_cfg::scoring_scheme{
                     seqan3::nucleotide_scoring_scheme{seqan3::match_score{4}, seqan3::mismatch_score{-5}}};
 
    auto seq1 = "ACGT"_dna4;
    auto seq2 = "ACCT"_dna4;
    for (auto res : align_pairwise(std::tie(seq1, seq2), min_cfg))
        seqan3::debug_stream << res.score() << '\n';
}

Constructor & Destructor Documentation

scoring_scheme()

template<std::semiregular scoring_scheme_t>

constexpr seqan3::align_cfg::scoring_scheme< scoring_scheme_t >::scoring_scheme ( scoring_scheme_t  scheme )

inlineexplicitconstexpr

Initialises the scoring scheme config with the given scheme.

Parameters

[in]

scheme

The scoring scheme to be used in the alignment algorithm.

This config stores a copy of the provided scheme.

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

• align_config_scoring_scheme.hpp