translate.hpp File Reference

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

#include <seqan3/std/concepts>
#include <seqan3/std/ranges>
#include <vector>
#include <stdexcept>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/alphabet/aminoacid/translation.hpp>
#include <seqan3/core/add_enum_bitwise_operators.hpp>
#include <seqan3/core/range/type_traits.hpp>
#include <seqan3/range/container/small_string.hpp>
#include <seqan3/range/detail/random_access_iterator.hpp>
#include <seqan3/range/views/deep.hpp>
#include <seqan3/range/views/detail.hpp>
#include <seqan3/range/container/concept.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
	seqan3
	The main SeqAn3 namespace.
	seqan3::detail
	The internal SeqAn3 namespace.
	seqan3::views
	The SeqAn namespace for views.

Enumerations
enum class	seqan3::translation_frames : uint8_t {   seqan3::FWD_FRAME_0 = 1 , seqan3::FWD_FRAME_1 = 1 << 1 , seqan3::FWD_FRAME_2 = 1 << 2 , seqan3::REV_FRAME_0 = 1 << 3 ,   seqan3::REV_FRAME_1 = 1 << 4 , seqan3::REV_FRAME_2 = 1 << 5 , seqan3::FWD_REV_0 = FWD_FRAME_0 | REV_FRAME_0 , seqan3::FWD_REV_1 = FWD_FRAME_1 | REV_FRAME_1 ,   seqan3::FWD_REV_2 = FWD_FRAME_2 | REV_FRAME_2 , seqan3::FWD = FWD_FRAME_0 | FWD_FRAME_1 | FWD_FRAME_2 , seqan3::REV = REV_FRAME_0 | REV_FRAME_1 | REV_FRAME_2 , seqan3::SIX_FRAME = FWD | REV }
	Specialisation values for single and multiple translation frames. More...

Functions
template<typename urng_t >
	seqan3::detail::view_translate (urng_t &&, translation_frames const =translation_frames{}) -> 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. More...
Alphabet related views
constexpr auto	seqan3::views::translate
	A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames. More...
constexpr auto	seqan3::views::translate_single
	A view that translates nucleotide into aminoacid alphabet for one of the six frames. More...

Detailed Description

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

Author

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