align_config_method.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, 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/algorithm/pipeable_config_element.hpp>
#include <seqan3/core/detail/empty_type.hpp>
#include <seqan3/core/detail/strong_type.hpp>
 
namespace seqan3::align_cfg
{
 
class method_local : public pipeable_config_element<method_local>
{
public:
    method_local() = default; 
    method_local(method_local const &) = default; 
    method_local(method_local &&) = default; 
    method_local & operator=(method_local const &) = default; 
    method_local & operator=(method_local &&) = default; 
    ~method_local() = default; 
 
    static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::local};
};
 
struct free_end_gaps_sequence1_leading : public seqan3::detail::strong_type<bool, free_end_gaps_sequence1_leading>
{
    using base_t = seqan3::detail::strong_type<bool, free_end_gaps_sequence1_leading>;
    using base_t::base_t; // Import the base class constructors
};
 
struct free_end_gaps_sequence2_leading : public seqan3::detail::strong_type<bool, free_end_gaps_sequence2_leading>
{
    using base_t = seqan3::detail::strong_type<bool, free_end_gaps_sequence2_leading>;
    using base_t::base_t; // Import the base class constructors
};
 
struct free_end_gaps_sequence1_trailing : public seqan3::detail::strong_type<bool, free_end_gaps_sequence1_trailing>
{
    using base_t = seqan3::detail::strong_type<bool, free_end_gaps_sequence1_trailing>;
    using base_t::base_t; // Import the base class constructors
};
 
struct free_end_gaps_sequence2_trailing : public seqan3::detail::strong_type<bool, free_end_gaps_sequence2_trailing>
{
    using base_t = seqan3::detail::strong_type<bool, free_end_gaps_sequence2_trailing>;
    using base_t::base_t; // Import the base class constructors
};
 
class method_global : public pipeable_config_element<method_global>
{
public:
    method_global() = default; 
    method_global(method_global const &) = default; 
    method_global(method_global &&) = default; 
    method_global & operator=(method_global const &) = default; 
    method_global & operator=(method_global &&) = default; 
    ~method_global() = default; 
 
    constexpr method_global(seqan3::align_cfg::free_end_gaps_sequence1_leading free_sequence1_leading,
                            seqan3::align_cfg::free_end_gaps_sequence2_leading free_sequence2_leading,
                            seqan3::align_cfg::free_end_gaps_sequence1_trailing free_sequence1_trailing,
                            seqan3::align_cfg::free_end_gaps_sequence2_trailing free_sequence2_trailing) noexcept :
        free_end_gaps_sequence1_leading{free_sequence1_leading.get()},
        free_end_gaps_sequence2_leading{free_sequence2_leading.get()},
        free_end_gaps_sequence1_trailing{free_sequence1_trailing.get()},
        free_end_gaps_sequence2_trailing{free_sequence2_trailing.get()}
    {}
 
    bool free_end_gaps_sequence1_leading{false};
    bool free_end_gaps_sequence2_leading{false};
    bool free_end_gaps_sequence1_trailing{false};
    bool free_end_gaps_sequence2_trailing{false};
 
    static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::global};
};
 
} // namespace seqan3::align_cfg