policy_max_error.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/std/ranges>
 
#include <seqan3/search/detail/search_common.hpp>
#include <seqan3/search/detail/search_traits.hpp>
 
namespace seqan3::detail
{
 
struct policy_max_error
{
protected:
    search_cfg::max_error_total total{};
    search_cfg::max_error_substitution substitution{};
    search_cfg::max_error_insertion insertion{};
    search_cfg::max_error_deletion deletion{};
 
    bool only_max_error_total{false};
    bool has_max_error_total{false};
 
    policy_max_error() = default; 
    policy_max_error(policy_max_error const &) = default; 
    policy_max_error(policy_max_error &&) = default; 
    policy_max_error & operator=(policy_max_error const &) = default; 
    policy_max_error & operator=(policy_max_error &&) = default; 
    ~policy_max_error() = default; 
 
    template <typename configuration_t>
        requires is_type_specialisation_of_v<configuration_t, seqan3::configuration>
    explicit policy_max_error(configuration_t const & config)
    {
        using search_traits_t = search_traits<configuration_t>;
        only_max_error_total = search_traits_t::only_max_error_total;
        has_max_error_total = search_traits_t::has_max_error_total;
 
        total = config.get_or(search_cfg::max_error_total{search_cfg::error_count{0}});
        substitution = config.get_or(search_cfg::max_error_substitution{search_cfg::error_count{0}});
        insertion = config.get_or(search_cfg::max_error_insertion{search_cfg::error_count{0}});
        deletion = config.get_or(search_cfg::max_error_deletion{search_cfg::error_count{0}});
    }
 
    template <std::ranges::forward_range query_t>
    auto max_error_counts(query_t && query)
    {
        detail::search_param errors{0, 0, 0, 0}; // total, substitution, insertion, deletion
 
        [[maybe_unused]] auto query_size = std::ranges::size(query);
 
        errors.total = to_error_count(total.error, query_size);
        errors.substitution = to_error_count(substitution.error, query_size);
        errors.insertion = to_error_count(insertion.error, query_size);
        errors.deletion = to_error_count(deletion.error, query_size);
 
        // If only total is set, we set all other errors to the total limit.
        if (only_max_error_total)
            errors.substitution = errors.insertion = errors.deletion = errors.total;
        // If total is not set but any other field is set than use total as the sum of all set errors.
        else if (!has_max_error_total)
            errors.total = std::min<uint32_t>(255, errors.substitution + errors.insertion + errors.deletion);
 
        // Validate the error configuration.
        // Checks if the given thresholds for the configured errors are valid. Otherwise throws std::invalid_argument.
        if (errors.substitution > errors.total)
            throw std::invalid_argument{"The substitution error threshold is higher than the total error threshold."};
        if (errors.insertion > errors.total)
            throw std::invalid_argument{"The insertion error threshold is higher than the total error threshold."};
        if (errors.deletion > errors.total)
            throw std::invalid_argument{"The deletion error threshold is higher than the total error threshold."};
 
        return errors;
    }
 
private:
    uint8_t to_error_count(std::variant<search_cfg::error_count, search_cfg::error_rate> const & error_variant,
                            [[maybe_unused]] size_t const query_size)
    {
        return std::visit([&query_size] (auto error)
            {
                if constexpr (std::same_as<decltype(error), search_cfg::error_count>)
                    return error.get();
                else
                {
                    // check correct error rate values.
                    if (0.0 > error.get() || error.get() > 1.0)
                        throw std::invalid_argument{"Error rates must be between 0 and 1."};
 
                    // make sure that error rate can be saved as uint8_t, so it is not too big in terms of query size
                    uint8_t const calculated_error_count = std::clamp(error.get() * query_size, 0.0, 255.0);
                    return calculated_error_count;
                }
            }, error_variant);
    }
};
 
} // namespace seqan3::detail