SeqAn3 3.4.0
The Modern C++ library for sequence analysis.
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align_config_edit.hpp
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1// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
2// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
3// SPDX-License-Identifier: BSD-3-Clause
4
9
10#pragma once
11
12#include <seqan3/alignment/configuration/align_config_gap_cost_affine.hpp>
13#include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>
14#include <seqan3/alignment/scoring/hamming_scoring_scheme.hpp>
15#include <seqan3/core/configuration/configuration.hpp>
16
17namespace seqan3::align_cfg
18{
19
48inline constexpr configuration edit_scheme =
49 scoring_scheme{hamming_scoring_scheme{}} | gap_cost_affine{open_score{0}, extension_score{-1}};
50
51} // namespace seqan3::align_cfg
align_config_gap_cost_affine.hpp
Provides seqan3::align_config::gap_cost_affine.
align_config_scoring_scheme.hpp
Provides seqan3::align_cfg::scoring_scheme.
seqan3::align_cfg::scoring_scheme
Sets the scoring scheme for the alignment algorithm.
Definition align_config_scoring_scheme.hpp:42
seqan3::configuration
Collection of elements to configure an algorithm.
Definition configuration.hpp:42
seqan3::hamming_scoring_scheme
A scoring scheme that assigns a score of 0 to matching letters and -1 to mismatching letters.
Definition hamming_scoring_scheme.hpp:33
configuration.hpp
Provides seqan3::configuration and utility functions.
seqan3::align_cfg::edit_scheme
constexpr configuration edit_scheme
Shortcut for edit distance configuration.
Definition align_config_edit.hpp:48
hamming_scoring_scheme.hpp
Provides seqan3::hamming_scoring_scheme.
seqan3::align_cfg
A special sub namespace for the alignment configurations.
Definition align_config_band.hpp:22
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