translation.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 <tuple>
 
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/alphabet/aminoacid/translation_genetic_code.hpp>
#include <seqan3/alphabet/aminoacid/translation_details.hpp>
#include <seqan3/core/type_traits/range.hpp>
 
namespace seqan3
{
 
// forwards:
class dna4;
class dna5;
class dna15;
class rna4;
class rna5;
class rna15;
 
template <genetic_code gc = genetic_code::CANONICAL, nucleotide_alphabet nucl_type>
constexpr aa27 translate_triplet(nucl_type const & n1, nucl_type const & n2, nucl_type const & n3) noexcept
{
    if constexpr (std::same_as<nucl_type, dna4> || std::same_as<nucl_type, dna5> || std::same_as<nucl_type, dna15>)
    {
        // table exists for dna15 and is generated for dna4 and dna5 (compile time ok, because small)
        return seqan3::detail::translation_table<nucl_type, gc>::VALUE[to_rank(n1)][to_rank(n2)][to_rank(n3)];
    }
    else if constexpr (std::same_as<nucl_type, rna4> || std::same_as<nucl_type, rna5> || std::same_as<nucl_type, rna15>)
    {
        using rna2dna_t = std::conditional_t<std::same_as<nucl_type, rna4>,  dna4,
                          std::conditional_t<std::same_as<nucl_type, rna5>,  dna5,
                          std::conditional_t<std::same_as<nucl_type, rna15>, dna15, void>>>;
 
        // we can use dna's tables, because ranks are identical
        return seqan3::detail::translation_table<rna2dna_t, gc>::VALUE[to_rank(n1)][to_rank(n2)][to_rank(n3)];
    }
    else // composites or user defined nucleotide
    {
        // we cast to dna15; slightly slower run-time, but lot's of compile time saved for large alphabets.
        // (nucleotide types can be converted to dna15 by definition)
        return seqan3::detail::translation_table<dna15, gc>::VALUE[to_rank(static_cast<dna15>(n1))]
                                                                  [to_rank(static_cast<dna15>(n2))]
                                                                  [to_rank(static_cast<dna15>(n3))];
    }
}
 
template <genetic_code gc = genetic_code::CANONICAL, typename tuple_type>
    requires std::tuple_size<tuple_type>::value == 3 &&
             nucleotide_alphabet<std::tuple_element_t<0, tuple_type>> &&
             nucleotide_alphabet<std::tuple_element_t<1, tuple_type>> &&
             nucleotide_alphabet<std::tuple_element_t<2, tuple_type>>
constexpr aa27 translate_triplet SEQAN3_DEPRECATED_310 (tuple_type const & input_tuple) noexcept
{
    return translate_triplet(std::get<0>(input_tuple), std::get<1>(input_tuple), std::get<2>(input_tuple));
}
 
template <genetic_code gc = genetic_code::CANONICAL, std::ranges::input_range range_type>
    requires nucleotide_alphabet<reference_t<std::decay_t<range_type>>>
constexpr aa27 translate_triplet SEQAN3_DEPRECATED_310 (range_type && input_range)
{
    auto n1 = begin(input_range);
    auto n2 = ++n1;
    auto n3 = ++n2;
 
    assert(n1 != end(input_range));
    assert(n2 != end(input_range));
    assert(n3 != end(input_range));
 
    return translate_triplet(*n1, *n2, *n3);
}
 
template <genetic_code gc = genetic_code::CANONICAL, std::ranges::random_access_range rng_t>
    requires nucleotide_alphabet<reference_t<std::decay_t<rng_t>>>
constexpr aa27 translate_triplet SEQAN3_DEPRECATED_310 (rng_t && input_range)
{
    assert(input_range.begin() != end(input_range));
    assert(input_range.begin() + 1 != end(input_range));
    assert(input_range.begin() + 2 != end(input_range));
 
    return translate_triplet(input_range[0], input_range[1], input_range[2]);
}
 
} // namespace seqan3