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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 | ||
| // ----------------------------------------------------------------------------------------------------- | ||
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| /*!\file | ||
| * \brief Provides seqan3::structure_record. | ||
| * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de> | ||
| */ | ||
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| #pragma once | ||
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| #include <seqan3/io/record.hpp> | ||
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| namespace seqan3 | ||
| { | ||
| /*!\brief The record type of seqan3::structure_file_input. | ||
| * \ingroup structure_file | ||
| * \implements seqan3::detail::record_like | ||
| * \tparam field_types The types of the fields in this record as a seqan3::type_list. | ||
| * \tparam field_ids A seqan3::fields type with seqan3::field IDs corresponding to field_types. | ||
| */ | ||
| template <typename field_types, typename field_ids> | ||
| class structure_record : public record<field_types, field_ids> | ||
| { | ||
| //!\brief The base class. | ||
| using base_t = record<field_types, field_ids>; | ||
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| //!\brief The underlying std::tuple class. | ||
| using tuple_base_t = typename base_t::base_type; | ||
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| //!\copydoc seqan3::record::field_constant | ||
| template <field f> | ||
| using field_constant = typename base_t::template field_constant<f>; | ||
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| using base_t::get_impl; | ||
| public: | ||
| /*!\name Constructors, destructor and assignment | ||
| * \{ | ||
| */ | ||
| structure_record() = default; //!< Defaulted. | ||
| structure_record(structure_record const &) = default; //!< Defaulted. | ||
| structure_record & operator=(structure_record const &) = default; //!< Defaulted. | ||
| structure_record(structure_record &&) = default; //!< Defaulted. | ||
| structure_record & operator=(structure_record &&) = default; //!< Defaulted. | ||
| ~structure_record() = default; //!< Defaulted. | ||
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| //!\brief Inherit std::tuple's and seqan3::record constructors. | ||
| using base_t::base_t; | ||
| //!\} | ||
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| //!\brief The identifier, usually a string. | ||
| decltype(auto) id() && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::id | ||
| decltype(auto) id() const && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t const &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::id | ||
| decltype(auto) id() & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t &>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::id | ||
| decltype(auto) id() const & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t const &>(*this)); | ||
| } | ||
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| //!\brief The "sequence", usually a range of nucleotides or amino acids. | ||
| decltype(auto) sequence() && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::sequence | ||
| decltype(auto) sequence() const && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t const &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::sequence | ||
| decltype(auto) sequence() & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t &>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::sequence | ||
| decltype(auto) sequence() const & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t const &>(*this)); | ||
| } | ||
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| //!\brief Fixed interactions, usually a string of structure alphabet characters. | ||
| decltype(auto) sequence_structure() && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::structure>{}, static_cast<tuple_base_t &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::sequence_structure | ||
| decltype(auto) sequence_structure() const && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::structure>{}, static_cast<tuple_base_t const &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::sequence_structure | ||
| decltype(auto) sequence_structure() & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::structure>{}, static_cast<tuple_base_t &>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::sequence_structure | ||
| decltype(auto) sequence_structure() const & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::structure>{}, static_cast<tuple_base_t const &>(*this)); | ||
| } | ||
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| //!\brief Energy of a folded sequence, represented by one float number. | ||
| decltype(auto) energy() && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::energy>{}, static_cast<tuple_base_t &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::energy | ||
| decltype(auto) energy() const && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::energy>{}, static_cast<tuple_base_t const &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::energy | ||
| decltype(auto) energy() & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::energy>{}, static_cast<tuple_base_t &>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::energy | ||
| decltype(auto) energy() const & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::energy>{}, static_cast<tuple_base_t const &>(*this)); | ||
| } | ||
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| //!\brief Base pair probability matrix of interactions, usually a matrix of float numbers. | ||
| decltype(auto) base_pair_probability_matrix() && | ||
| { | ||
| // this is computed | ||
| return get_impl(field_constant<seqan3::field::bpp>{}, static_cast<tuple_base_t &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::base_pair_probability_matrix | ||
| decltype(auto) base_pair_probability_matrix() const && | ||
| { | ||
| return get_impl(field_constant<seqan3::field::bpp>{}, static_cast<tuple_base_t const &&>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::base_pair_probability_matrix | ||
| decltype(auto) base_pair_probability_matrix() & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::bpp>{}, static_cast<tuple_base_t &>(*this)); | ||
| } | ||
| //!\copydoc seqan3::structure_record::base_pair_probability_matrix | ||
| decltype(auto) base_pair_probability_matrix() const & | ||
| { | ||
| return get_impl(field_constant<seqan3::field::bpp>{}, static_cast<tuple_base_t const &>(*this)); | ||
| } | ||
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| // decltype(auto) reactivity(); // unused | ||
| // decltype(auto) reactivity_errors(); // unused | ||
| // decltype(auto) comment(); // unused | ||
| // decltype(auto) base_qualities(); // unused | ||
| }; | ||
| } // namespace seqan3 | ||
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| namespace std | ||
| { | ||
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| /*!\brief Provides access to the number of elements in a tuple as a compile-time constant expression. | ||
| * \implements seqan3::unary_type_trait | ||
| * \relates seqan3::structure_record | ||
| * \see std::tuple_size_v | ||
| */ | ||
| template <typename field_types, typename field_ids> | ||
| struct tuple_size<seqan3::structure_record<field_types, field_ids>> | ||
| : tuple_size<typename seqan3::structure_record<field_types, field_ids>::base_type> | ||
| {}; | ||
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| /*!\brief Obtains the type of the specified element. | ||
| * \implements seqan3::transformation_trait | ||
| * \relates seqan3::structure_record | ||
| * \see [std::tuple_element](https://en.cppreference.com/w/cpp/utility/tuple/tuple_element) | ||
| */ | ||
| template <size_t elem_no, typename field_types, typename field_ids> | ||
| struct tuple_element<elem_no, seqan3::structure_record<field_types, field_ids>> | ||
| : tuple_element<elem_no, typename seqan3::structure_record<field_types, field_ids>::base_type> | ||
| {}; | ||
|
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| } // namespace std |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| seqan3_test(format_vienna_test.cpp) | ||
| seqan3_test(structure_file_input_test.cpp) | ||
| seqan3_test(structure_file_output_test.cpp) | ||
| seqan3_test(structure_file_record_test.cpp) |
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