policy_scoring_scheme.hpp

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// -----------------------------------------------------------------------------------------------------
// 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/align_config_scoring_scheme.hpp>
#include <seqan3/core/configuration/configuration.hpp>
#include <seqan3/utility/simd/concept.hpp>
 
namespace seqan3::detail
{
 
template <typename alignment_configuration_t, typename scoring_scheme_t>
class policy_scoring_scheme
{
protected:
    scoring_scheme_t scoring_scheme{};
 
    policy_scoring_scheme() = default;                                          
    policy_scoring_scheme(policy_scoring_scheme const &) = default;             
    policy_scoring_scheme(policy_scoring_scheme &&) = default;                  
    policy_scoring_scheme & operator=(policy_scoring_scheme const &) = default; 
    policy_scoring_scheme & operator=(policy_scoring_scheme &&) = default;      
    ~policy_scoring_scheme() = default;                                         
 
    explicit policy_scoring_scheme(alignment_configuration_t const & config) :
        scoring_scheme{seqan3::get<align_cfg::scoring_scheme>(config).scheme}
    {}
 
    template <typename alphabet_t>
        requires simd_concept<std::remove_cvref_t<alphabet_t>>
    auto scoring_scheme_profile_column(alphabet_t && alphabet) const noexcept
    {
        return scoring_scheme.make_score_profile(std::forward<alphabet_t>(alphabet));
    }
 
    template <semialphabet alphabet_t>
    alphabet_t scoring_scheme_profile_column(alphabet_t && alphabet) const noexcept
    {
        return std::forward<alphabet_t>(alphabet);
    }
};
 
} // namespace seqan3::detail