translate.hpp File Reference

Provides seqan3::views::translate and seqan3::views::translate_single. More...

#include <concepts>
#include <ranges>
#include <stdexcept>
#include <vector>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/alphabet/aminoacid/translation.hpp>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/core/add_enum_bitwise_operators.hpp>
#include <seqan3/core/range/detail/adaptor_from_functor.hpp>
#include <seqan3/core/range/type_traits.hpp>
#include <seqan3/utility/container/small_string.hpp>
#include <seqan3/utility/views/deep.hpp>

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Classes
struct	seqan3::detail::translate_fn< single >
	Definition of the range adaptor object type for seqan3::views::translate and seqan3::views::translate_single. More...
class	seqan3::detail::view_translate< urng_t >
	The return type of seqan3::views::translate. More...
class	seqan3::detail::view_translate_single< urng_t >
	The return type of seqan3::views::translate_single. More...

Namespaces
namespace	seqan3
	The main SeqAn3 namespace.
namespace	seqan3::detail
	The internal SeqAn3 namespace.
namespace	seqan3::views
	The SeqAn namespace for views.

Enumerations
enum class	seqan3::translation_frames : uint8_t {   seqan3::forward_frame0 = 1 , seqan3::forward_frame1 = 1 << 1 , seqan3::forward_frame2 = 1 << 2 , seqan3::reverse_frame0 = 1 << 3 ,   seqan3::reverse_frame1 = 1 << 4 , seqan3::reverse_frame2 = 1 << 5 , seqan3::forward_reverse0 = forward_frame0 | reverse_frame0 , seqan3::forward_reverse1 = forward_frame1 | reverse_frame1 ,   seqan3::forward_reverse2 = forward_frame2 | reverse_frame2 , seqan3::forward_frames = forward_frame0 | forward_frame1 | forward_frame2 , seqan3::reverse_frames = reverse_frame0 | reverse_frame1 | reverse_frame2 , seqan3::six_frames = forward_frames | reverse_frames }
	Specialisation values for single and multiple translation frames. More...

Functions
template<typename urng_t > requires std::ranges::sized_range<urng_t> && std::ranges::random_access_range<urng_t> && nucleotide_alphabet<std::ranges::range_reference_t<urng_t>>
	seqan3::detail::view_translate (urng_t &&, translation_frames const) -> view_translate< std::views::all_t< urng_t > >
	Class template argument deduction for view_translate.
template<typename urng_t >
	seqan3::detail::view_translate_single (urng_t &&) -> view_translate_single< std::views::all_t< urng_t > >
	Class template argument deduction for view_translate_single with default translation_frames.
template<typename urng_t >
	seqan3::detail::view_translate_single (urng_t &&, translation_frames const) -> view_translate_single< std::views::all_t< urng_t > >
	Class template argument deduction for view_translate_single.

Variables
template<>
constexpr bool	seqan3::add_enum_bitwise_operators< translation_frames > = true
	Enable bitwise operators for enum translation_frames.
constexpr auto	seqan3::views::translate
	A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames.
Alphabet related views
constexpr auto	seqan3::views::translate_single
	A view that translates nucleotide into aminoacid alphabet for one of the six frames.

Detailed Description

Provides seqan3::views::translate and seqan3::views::translate_single.

Author

Sara Hetzel <sara.hetzel AT fu-berlin.de>