seqan3::align_cfg::gap_cost_affine Class Reference

A configuration element for the affine gap cost scheme. More...

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

Inheritance diagram for seqan3::align_cfg::gap_cost_affine:

Public Member Functions
Constructors, destructor and assignment
constexpr	gap_cost_affine ()=default
	Defaulted.
constexpr	gap_cost_affine (gap_cost_affine const &)=default
	Defaulted.
constexpr	gap_cost_affine (gap_cost_affine &&)=default
	Defaulted.
constexpr gap_cost_affine &	operator= (gap_cost_affine const &)=default
	Defaulted.
constexpr gap_cost_affine &	operator= (gap_cost_affine &&)=default
	Defaulted.
	~gap_cost_affine ()=default
	Defaulted.
constexpr	gap_cost_affine (seqan3::align_cfg::open_score open_score, seqan3::align_cfg::extension_score extension_score)
	Construction from strongly typed open score and extension score.

Public Attributes
int32_t	extension_score {-1}
	The cost per gap character. Defaults to -1.
int32_t	open_score {0}
	The score per consecutive sequence of gaps. Defaults to 0.

Detailed Description

A configuration element for the affine gap cost scheme.

Configures the gap scheme for the alignment algorithm. The gap scheme determines how gaps are penalised inside of the alignment algorithm. If the gap scheme is not configured, it will default to a linear gap scheme initialised with edit distance. Note that the gap open score is used as an additional score. This means that the score for opening a gap during the affine alignment execution is the sum of the gap score and the gap open score.

See also

seqan3::align_cfg::method_global

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 <iostream>
 
#include <seqan3/alignment/configuration/align_config_gap_cost_affine.hpp>
 
int main()
{
    // Configuration with linear gap costs.
    seqan3::align_cfg::gap_cost_affine linear_cfg{seqan3::align_cfg::open_score{0},
                                                  seqan3::align_cfg::extension_score{-1}};
 
    // Configuration with affine gap costs. Score for opening a gap during the alignment algorithm will be -11.
    seqan3::align_cfg::gap_cost_affine affine_cfg{seqan3::align_cfg::open_score{-1},
                                                  seqan3::align_cfg::extension_score{-10}};
 
    // Accessing the members of the gap scheme
    int open = affine_cfg.open_score;
    int extension = affine_cfg.extension_score;
    std::cout << open << '\n';      // -1
    std::cout << extension << '\n'; // -10
}

Constructor & Destructor Documentation

gap_cost_affine()

constexpr seqan3::align_cfg::gap_cost_affine::gap_cost_affine ( seqan3::align_cfg::open_score  open_score, seqan3::align_cfg::extension_score  extension_score  )

inlineconstexpr

Construction from strongly typed open score and extension score.

Parameters

open_score	The cost per consecutive sequence of gaps (of type seqan3::open_score).
extension_score	The cost of each gap character (of type seqan3::extension_score).

The score for a sequence of n gap characters is computed as open_score + n * extension_score.

Attention

This is the formula used most commonly in the literature, but it is different from SeqAn2 where the formula was (n-1) * extension_score + open_score.

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

• align_config_gap_cost_affine.hpp