affine_gap_init_policy.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
 
#pragma once
 
#include <tuple>
 
#include <seqan3/alignment/configuration/align_config_method.hpp>
#include <seqan3/alignment/matrix/detail/trace_directions.hpp>
#include <seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp>
 
namespace seqan3::detail
{
 
template <typename alignment_algorithm_t>
class affine_gap_init_policy
{
private:
    friend alignment_algorithm_t;
 
    bool first_row_is_free{};
    bool first_column_is_free{};
 
    constexpr affine_gap_init_policy() noexcept = default;                                           
    constexpr affine_gap_init_policy(affine_gap_init_policy const &) noexcept = default;             
    constexpr affine_gap_init_policy(affine_gap_init_policy &&) noexcept = default;                  
    constexpr affine_gap_init_policy & operator=(affine_gap_init_policy const &) noexcept = default; 
    constexpr affine_gap_init_policy & operator=(affine_gap_init_policy &&) noexcept = default;      
    ~affine_gap_init_policy() noexcept = default;                                                    
 
    template <typename config_t>
    affine_gap_init_policy(config_t const & config)
    {
        bool is_local = config.template exists<align_cfg::method_local>();
        auto method_global_config = config.get_or(align_cfg::method_global{});
        first_row_is_free = method_global_config.free_end_gaps_sequence1_leading | is_local;
        first_column_is_free = method_global_config.free_end_gaps_sequence2_leading | is_local;
    }
 
    template <typename cell_t, typename score_t>
    constexpr auto init_origin_cell(cell_t && origin_cell, alignment_algorithm_state<score_t> & state) const noexcept
    {
        // score_cell = seqan3::detail::alignment_score_matrix_proxy
        // trace_cell = seqan3::detail::alignment_trace_matrix_proxy
        auto & [score_cell, trace_cell] = origin_cell;
 
        // Initialise the first cell.
        score_cell.current = convert_to_simd_maybe<score_t>(0);
        trace_cell.current = convert_to_simd_maybe<score_t>(trace_directions::none);
 
        static_cast<alignment_algorithm_t const &>(*this).check_score_of_cell(origin_cell, state);
 
        // Initialise the vertical matrix cell according to the traits settings.
        if (first_column_is_free)
        {
            score_cell.up = convert_to_simd_maybe<score_t>(0);
            trace_cell.up = convert_to_simd_maybe<score_t>(trace_directions::none);
        }
        else // Initialise with gap_open score
        {
            score_cell.up = state.gap_open_score;
            trace_cell.up = convert_to_simd_maybe<score_t>(trace_directions::up_open);
        }
 
        // Initialise the horizontal matrix cell according to the traits settings.
        if (first_row_is_free)
        {
            score_cell.w_left = convert_to_simd_maybe<score_t>(0);
            trace_cell.w_left = convert_to_simd_maybe<score_t>(trace_directions::none);
        }
        else // Initialise with gap_open score
        {
            score_cell.w_left = state.gap_open_score;
            trace_cell.w_left = convert_to_simd_maybe<score_t>(trace_directions::left_open);
        }
    }
 
    template <typename cell_t, typename score_t>
    constexpr auto init_column_cell(cell_t && column_cell, alignment_algorithm_state<score_t> & state) const noexcept
    {
        // score_cell = seqan3::detail::alignment_score_matrix_proxy
        // trace_cell = seqan3::detail::alignment_trace_matrix_proxy
        auto & [score_cell, trace_cell] = column_cell;
 
        score_cell.current = score_cell.up;
        trace_cell.current = trace_cell.up;
 
        static_cast<alignment_algorithm_t const &>(*this).check_score_of_cell(column_cell, state);
 
        // Initialise the vertical matrix cell according to the traits settings.
        if (first_column_is_free)
        {
            score_cell.up = convert_to_simd_maybe<score_t>(0);
        }
        else
        {
            score_cell.up += state.gap_extension_score;
            trace_cell.up = convert_to_simd_maybe<score_t>(trace_directions::up);
        }
 
        score_cell.w_left = score_cell.current + state.gap_open_score;
        trace_cell.w_left = convert_to_simd_maybe<score_t>(trace_directions::left_open);
    }
 
    template <typename cell_t, typename score_t>
    constexpr auto init_row_cell(cell_t && row_cell, alignment_algorithm_state<score_t> & state) const noexcept
    {
        // score_cell = seqan3::detail::alignment_score_matrix_proxy
        // trace_cell = seqan3::detail::alignment_trace_matrix_proxy
        auto & [score_cell, trace_cell] = row_cell;
 
        score_cell.current = score_cell.r_left;
        trace_cell.current = trace_cell.r_left;
 
        static_cast<alignment_algorithm_t const &>(*this).check_score_of_cell(row_cell, state);
 
        score_cell.up = score_cell.current + state.gap_open_score;
        trace_cell.up = convert_to_simd_maybe<score_t>(trace_directions::up_open);
 
        if (first_row_is_free)
        {
            score_cell.w_left = convert_to_simd_maybe<score_t>(0);
            trace_cell.w_left = convert_to_simd_maybe<score_t>(trace_directions::none);
        }
        else
        {
            score_cell.w_left = score_cell.r_left + state.gap_extension_score;
            trace_cell.w_left = convert_to_simd_maybe<score_t>(trace_directions::left);
        }
    }
 
private:
    template <typename score_t, typename value_t>
    constexpr auto convert_to_simd_maybe(value_t const value) const noexcept
    {
        if constexpr (simd_concept<score_t>)
        {
            using scalar_t = typename simd_traits<score_t>::scalar_type;
            return simd::fill<score_t>(static_cast<scalar_t>(value));
        }
        else
        {
            return value;
        }
    }
};
 
} // namespace seqan3::detail