edit_distance_fwd.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/align_config_min_score.hpp>
#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/alignment/pairwise/align_result_selector.hpp>
#include <seqan3/core/bit_manipulation.hpp>
#include <seqan3/core/platform.hpp>
#include <seqan3/core/type_traits/deferred_crtp_base.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/ranges>
 
namespace seqan3::detail
{
template <typename word_t, typename score_t, bool is_semi_global, bool use_max_errors>
class edit_distance_score_matrix_full; //forward declaration
 
template <typename word_t, bool is_semi_global, bool use_max_errors>
class edit_distance_trace_matrix_full; //forward declaration
 
template <typename state_t, typename ...>
struct empty_state
{};
 
template <bool enabled, typename state_t>
using enable_state_t = std::conditional_t<enabled, state_t, empty_state<state_t>>;
 
template <bool B, template <typename ...> typename T, template <typename ...> typename F>
struct selector
{
    template <typename ...args_t>
    struct select : public std::conditional_t<B, T<args_t...>, F<args_t...>>
    {};
};
 
template <std::ranges::viewable_range database_t,
          std::ranges::viewable_range query_t,
          typename align_config_t,
          typename is_semi_global_t,
          typename word_t = uint_fast64_t>
struct default_edit_distance_trait_type
{
    using align_config_type = std::remove_reference_t<align_config_t>;
    using alignment_traits_type = alignment_configuration_traits<align_config_type>;
    using word_type = word_t;
    static_assert(std::is_unsigned_v<word_type>, "the word type of edit_distance_unbanded must be unsigned.");
    static_assert(alignment_traits_type::has_output_configuration, "We assume the result type was configured.");
    using score_type = typename alignment_traits_type::original_score_type;
    using database_type = std::remove_reference_t<database_t>;
    using query_type = std::remove_reference_t<query_t>;
 
    static constexpr uint8_t word_size = sizeof_bits<word_type>;
    static_assert(sizeof_bits<word_type> <= 64u, "we assume at most uint64_t as word_type");
 
    using database_iterator = std::ranges::iterator_t<database_type>;
    using query_alphabet_type = std::remove_reference_t<std::ranges::range_reference_t<query_type>>;
    using alignment_result_type = typename alignment_traits_type::alignment_result_type;
    using result_value_type = typename alignment_result_value_type_accessor<alignment_result_type>::type;
 
    static constexpr bool use_max_errors = align_config_type::template exists<align_cfg::min_score>();
    static constexpr bool is_semi_global = is_semi_global_t::value;
    static constexpr bool is_global = !is_semi_global;
    static constexpr bool compute_score = true;
    static constexpr bool compute_sequence_alignment = alignment_traits_type::compute_sequence_alignment;
    static constexpr bool compute_begin_positions = alignment_traits_type::compute_begin_positions ||
                                                    compute_sequence_alignment;
    static constexpr bool compute_end_positions = alignment_traits_type::compute_end_positions ||
                                                  compute_begin_positions;
    static constexpr bool compute_score_matrix = false;
    static constexpr bool compute_trace_matrix = compute_begin_positions || compute_sequence_alignment;
    static constexpr bool compute_matrix = compute_score_matrix || compute_trace_matrix;
 
    using trace_matrix_type = edit_distance_trace_matrix_full<word_type, is_semi_global, use_max_errors>;
    using score_matrix_type = edit_distance_score_matrix_full<word_type, score_type, is_semi_global, use_max_errors>;
};
 
template <bool enable_policy,
          template <typename ...> typename policy_t,
          typename edit_traits,
          typename derived_t>
using edit_distance_base =
    invoke_deferred_crtp_base<deferred_crtp_base<selector<enable_policy, policy_t, empty_state>::template select,
                                                 edit_traits>,
                              derived_t>;
 
template <std::ranges::viewable_range database_t,
          std::ranges::viewable_range query_t,
          typename align_config_t,
          typename traits_t>
class edit_distance_unbanded; //forward declaration
 
} // namespace seqan3::detail