align_config_gap_cost_affine.hpp

Go to the documentation of this file.

// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2022, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <seqan3/alignment/configuration/detail.hpp>
#include <seqan3/core/configuration/pipeable_config_element.hpp>
#include <seqan3/core/detail/strong_type.hpp>
 
namespace seqan3::align_cfg
{
// ------------------------------------------------------------------
// seqan3::align_cfg::open_score
// ------------------------------------------------------------------
 
struct open_score : seqan3::detail::strong_type<int32_t, open_score, seqan3::detail::strong_type_skill::convert>
{
    using base_t = seqan3::detail::strong_type<int32_t, open_score, seqan3::detail::strong_type_skill::convert>;
    using base_t::base_t; // Import the base class constructors
};
 
// ------------------------------------------------------------------
// seqan3::align_cfg::extension_score
// ------------------------------------------------------------------
 
struct extension_score :
    seqan3::detail::strong_type<int32_t, extension_score, seqan3::detail::strong_type_skill::convert>
{
    using base_t = seqan3::detail::strong_type<int32_t, extension_score, seqan3::detail::strong_type_skill::convert>;
    using base_t::base_t; // Import the base class constructors
};
 
class gap_cost_affine : private pipeable_config_element
{
public:
    int32_t open_score{0};
    int32_t extension_score{-1};
 
    constexpr gap_cost_affine() = default;                                    
    constexpr gap_cost_affine(gap_cost_affine const &) = default;             
    constexpr gap_cost_affine(gap_cost_affine &&) = default;                  
    constexpr gap_cost_affine & operator=(gap_cost_affine const &) = default; 
    constexpr gap_cost_affine & operator=(gap_cost_affine &&) = default;      
    ~gap_cost_affine() = default;                                             
 
    constexpr gap_cost_affine(seqan3::align_cfg::open_score open_score,
                              seqan3::align_cfg::extension_score extension_score) :
        open_score(std::move(open_score)),
        extension_score(std::move(extension_score))
    {}
 
    static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::gap};
};
 
} // namespace seqan3::align_cfg