33namespace seqan3::detail
36template <std::ranges::view urng_t>
37 requires std::ranges::sized_range<urng_t> && std::ranges::random_access_range<urng_t>
41template <std::ranges::view urng_t>
42 requires std::ranges::sized_range<urng_t> && std::ranges::random_access_range<urng_t>
44class view_translate_single;
81constexpr bool add_enum_bitwise_operators<translation_frames> =
true;
86namespace seqan3::detail
106 return detail::adaptor_from_functor{*
this, tf};
114 template <std::ranges::range urng_t>
115 constexpr auto operator()(urng_t && urange,
translation_frames const tf = default_frames)
const
117 static_assert(std::ranges::viewable_range<urng_t>,
118 "The range parameter to views::translate[_single] cannot be a temporary of a non-view range.");
119 static_assert(std::ranges::sized_range<urng_t>,
120 "The range parameter to views::translate[_single] must model std::ranges::sized_range.");
121 static_assert(std::ranges::random_access_range<urng_t>,
122 "The range parameter to views::translate[_single] must model std::ranges::random_access_range.");
125 "The range parameter to views::translate[_single] must be over elements of seqan3::nucleotide_alphabet.");
128 return detail::view_translate_single{std::forward<urng_t>(urange), tf};
130 return detail::view_translate{std::forward<urng_t>(urange), tf};
134 template <std::ranges::range urng_t>
135 constexpr friend auto operator|(urng_t && urange, translate_fn
const & me)
137 return me(std::forward<urng_t>(urange));
151template <std::ranges::view urng_t>
152 requires std::ranges::sized_range<urng_t> && std::ranges::random_access_range<urng_t>
154class view_translate_single :
public std::ranges::view_base
162 static constexpr small_string multiple_frame_error{
"Error: Invalid type of frame. Choose one out of "
163 "forward_frame0, reverse_frame0, forward_frame1, "
164 "reverse_frame1, forward_frame2 and reverse_frame2."};
171 using reference = aa27;
173 using const_reference = aa27;
175 using value_type = aa27;
177 using size_type = std::ranges::range_size_t<urng_t>;
179 using difference_type = std::ranges::range_difference_t<urng_t>;
181 using iterator = detail::random_access_iterator<view_translate_single>;
183 using const_iterator = detail::random_access_iterator<view_translate_single const>;
189 view_translate_single() noexcept = default;
190 constexpr view_translate_single(view_translate_single const & rhs) noexcept = default;
191 constexpr view_translate_single(view_translate_single && rhs) noexcept = default;
192 constexpr view_translate_single & operator=(view_translate_single const & rhs) noexcept = default;
193 constexpr view_translate_single & operator=(view_translate_single && rhs) noexcept = default;
194 ~view_translate_single() noexcept = default;
205 urange{std::move(_urange)},
208 if (__builtin_popcount(
static_cast<uint8_t
>(_tf)) > 1)
222 template <
typename rng_t>
223 requires (!std::same_as<std::remove_cvref_t<rng_t>, view_translate_single>)
224 && std::ranges::viewable_range<rng_t>
227 view_translate_single{std::views::all(std::forward<rng_t>(_urange)), _tf}
247 iterator
begin() noexcept
253 const_iterator
begin() const noexcept
271 iterator
end() noexcept
273 return {*
this,
size()};
277 const_iterator
end() const noexcept
279 return {*
this,
size()};
320 size_type
size()
const
363 reference operator[](size_type
const n)
380 return translate_triplet((urange)[n * 3], (urange)[n * 3 + 1], (urange)[n * 3 + 2]);
388 return translate_triplet((urange)[n * 3 + 1], (urange)[n * 3 + 2], (urange)[n * 3 + 3]);
396 return translate_triplet((urange)[n * 3 + 2], (urange)[n * 3 + 3], (urange)[n * 3 + 4]);
410 const_reference operator[](size_type
const n)
const
427 return translate_triplet((urange)[n * 3], (urange)[n * 3 + 1], (urange)[n * 3 + 2]);
435 return translate_triplet((urange)[n * 3 + 1], (urange)[n * 3 + 2], (urange)[n * 3 + 3]);
443 return translate_triplet((urange)[n * 3 + 2], (urange)[n * 3 + 3], (urange)[n * 3 + 4]);
459template <
typename urng_t>
460view_translate_single(urng_t &&,
translation_frames const) -> view_translate_single<std::views::all_t<urng_t>>;
463template <
typename urng_t>
464view_translate_single(urng_t &&) -> view_translate_single<std::views::all_t<urng_t>>;
531namespace seqan3::detail
542template <std::ranges::view urng_t>
543 requires std::ranges::sized_range<urng_t> && std::ranges::random_access_range<urng_t>
545class view_translate :
public std::ranges::view_base
553 small_vector<translation_frames, 6> selected_frames{};
560 using reference = view_translate_single<urng_t>;
562 using const_reference = reference;
564 using value_type = reference;
566 using size_type = std::ranges::range_size_t<urng_t>;
568 using difference_type = std::ranges::range_difference_t<urng_t>;
570 using iterator = detail::random_access_iterator<view_translate>;
572 using const_iterator = detail::random_access_iterator<view_translate const>;
583 template <
typename t>
584 requires (range_dimension_v<t> == range_dimension_v<value_type> + 1)
587 static constexpr bool is_compatible_this_aux =
true;
595 view_translate() noexcept = default;
596 constexpr view_translate(view_translate const & rhs) noexcept = default;
597 constexpr view_translate(view_translate && rhs) noexcept = default;
598 constexpr view_translate & operator=(view_translate const & rhs) noexcept = default;
599 constexpr view_translate & operator=(view_translate && rhs) noexcept = default;
600 ~view_translate() noexcept = default;
607 urange{std::move(_urange)},
628 template <
typename rng_t>
629 requires (!std::same_as<std::remove_cvref_t<rng_t>, view_translate>) && std::ranges::viewable_range<rng_t>
632 view_translate{std::views::all(std::forward<rng_t>(_urange)), _tf}
652 iterator
begin() noexcept
658 const_iterator
begin() const noexcept
676 iterator
end() noexcept
678 return {*
this,
size()};
682 const_iterator
end() const noexcept
684 return {*
this,
size()};
698 size_type
size() noexcept
700 return (size_type)selected_frames.size();
704 size_type
size() const noexcept
706 return (size_type)selected_frames.size();
727 reference operator[](size_type
const n)
734 const_reference operator[](size_type
const n)
const
743template <
typename urng_t>
744 requires std::ranges::sized_range<urng_t> && std::ranges::random_access_range<urng_t>
746 view_translate(urng_t &&,
translation_frames const) -> view_translate<std::views::all_t<urng_t>>;
Provides seqan3::aa27, container aliases and string literals.
Provides seqan3::detail::adaptor_from_functor.
Provides seqan3::add_enum_bitwise_operators.
A wrapper type around an existing view adaptor that enables "deep view" behaviour for that view.
Definition: deep.hpp:104
Provides various transformation traits used by the range module.
Provides seqan3::views::deep.
Provides seqan3::dna5, container aliases and string literals.
constexpr aa27 translate_triplet(nucl_type const &n1, nucl_type const &n2, nucl_type const &n3) noexcept
Translate one nucleotide triplet into single amino acid (single nucleotide interface).
Definition: translation.hpp:55
constexpr auto complement
Return the complement of a nucleotide object.
Definition: concept.hpp:105
constexpr auto translate
A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames.
Definition: translate.hpp:803
constexpr auto translate_single
A view that translates nucleotide into aminoacid alphabet for one of the six frames.
Definition: translate.hpp:523
auto operator|(validator1_type &&vali1, validator2_type &&vali2)
Enables the chaining of validators.
Definition: validators.hpp:1124
@ single
The text is a single range.
Definition: concept.hpp:93
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:146
A concept that indicates whether an alphabet represents nucleotides.
The SeqAn namespace for views.
Definition: char_strictly_to.hpp:22
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
translation_frames
Specialisation values for single and multiple translation frames.
Definition: translate.hpp:62
@ forward_frame2
The third forward frame starting at position 2.
@ forward_frame0
The first forward frame starting at position 0.
@ reverse_frames
All reverse frames.
@ forward_frames
All forward frames.
@ reverse_frame0
The first reverse frame starting at position 0.
@ forward_reverse2
The first third and third reverse frame.
@ reverse_frame2
The third reverse frame starting at position 2.
@ forward_frame1
The second forward frame starting at position 1.
@ reverse_frame1
The second reverse frame starting at position 1.
@ forward_reverse0
The first forward and first reverse frame.
@ forward_reverse1
The second forward and second reverse frame.
A constexpr string implementation to manipulate string literals at compile time.
Provides functions for translating a triplet of nucleotides into an amino acid.