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/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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Namespaces
	seqan3
	The main SeqAn3 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 ,   seqan3::FWD_FRAME_0 = forward_frame0 , seqan3::FWD_FRAME_1 = forward_frame1 , seqan3::FWD_FRAME_2 = forward_frame2 , seqan3::REV_FRAME_0 = reverse_frame0 ,   seqan3::REV_FRAME_1 = reverse_frame1 , seqan3::REV_FRAME_2 = reverse_frame2 , seqan3::FWD_REV_0 = forward_reverse0 , seqan3::FWD_REV_1 = forward_reverse1 ,   seqan3::FWD_REV_2 = forward_reverse2 , seqan3::FWD = forward_frames , seqan3::REV = reverse_frames , seqan3::SIX_FRAME = six_frames }
	Specialisation values for single and multiple translation frames. More...

Variables
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>