policy_affine_gap_recursion_banded.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2021, 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/pairwise/detail/policy_affine_gap_recursion.hpp>
 
namespace seqan3::detail
{
 
template <typename alignment_configuration_t>
class policy_affine_gap_recursion_banded : protected policy_affine_gap_recursion<alignment_configuration_t>
{
protected:
    using base_t = policy_affine_gap_recursion<alignment_configuration_t>;
    // Import base types
    using typename base_t::traits_type;
    using typename base_t::score_type;
    using typename base_t::affine_cell_type;
 
    //Import member types.
    using base_t::gap_extension_score;
    using base_t::gap_open_score;
 
    policy_affine_gap_recursion_banded() = default; 
    policy_affine_gap_recursion_banded(policy_affine_gap_recursion_banded const &) = default; 
    policy_affine_gap_recursion_banded(policy_affine_gap_recursion_banded &&) = default; 
    policy_affine_gap_recursion_banded & operator=(policy_affine_gap_recursion_banded const &) = default; 
    policy_affine_gap_recursion_banded & operator=(policy_affine_gap_recursion_banded &&) = default; 
    ~policy_affine_gap_recursion_banded() = default; 
 
    explicit policy_affine_gap_recursion_banded(alignment_configuration_t const & config) : base_t{config}
    {}
 
    template <typename affine_cell_t>
    affine_cell_type initialise_band_first_cell(score_type diagonal_score,
                                                affine_cell_t previous_cell,
                                                score_type const sequence_score) const noexcept
    {
        diagonal_score += sequence_score;
        score_type horizontal_score = previous_cell.horizontal_score();
        diagonal_score = (diagonal_score < horizontal_score) ? horizontal_score : diagonal_score;
        score_type from_optimal_score = diagonal_score + gap_open_score;
        horizontal_score += gap_extension_score;
        horizontal_score = (horizontal_score < from_optimal_score) ? from_optimal_score : horizontal_score;
        return {diagonal_score, horizontal_score, from_optimal_score};
    }
};
} // namespace seqan3::detail