35 namespace seqan3::detail
38 template <std::ranges::view urng_t>
40 requires std::ranges::sized_range<urng_t> &&
41 std::ranges::random_access_range<urng_t> &&
46 template <std::ranges::view urng_t>
48 requires std::ranges::sized_range<urng_t> &&
49 std::ranges::random_access_range<urng_t> &&
52 class view_translate_single;
86 namespace seqan3::detail
96 template <
bool single>
107 return detail::adaptor_from_functor{*
this, tf};
115 template <std::ranges::range urng_t>
116 constexpr
auto operator()(urng_t && urange,
translation_frames const tf = default_frames)
const
118 static_assert(std::ranges::viewable_range<urng_t>,
119 "The range parameter to views::translate[_single] cannot be a temporary of a non-view range.");
120 static_assert(std::ranges::sized_range<urng_t>,
121 "The range parameter to views::translate[_single] must model std::ranges::sized_range.");
122 static_assert(std::ranges::random_access_range<urng_t>,
123 "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));
151 template <std::ranges::view urng_t>
153 requires std::ranges::sized_range<urng_t> &&
154 std::ranges::random_access_range<urng_t> &&
157 class view_translate_single :
public std::ranges::view_base
165 static constexpr small_string multiple_frame_error{
"Error: Invalid type of frame. Choose one out of FWD_FRAME_0, "
166 "REV_FRAME_0, FWD_FRAME_1, REV_FRAME_1, FWD_FRAME_2 and "
173 using reference = aa27;
175 using const_reference = aa27;
177 using value_type = aa27;
179 using size_type = std::ranges::range_size_t<urng_t>;
181 using difference_type = std::ranges::range_difference_t<urng_t>;
183 using iterator = detail::random_access_iterator<view_translate_single>;
185 using const_iterator = detail::random_access_iterator<view_translate_single const>;
191 view_translate_single() noexcept = default;
192 constexpr view_translate_single(view_translate_single const & rhs) noexcept = default;
193 constexpr view_translate_single(view_translate_single && rhs) noexcept = default;
194 constexpr view_translate_single & operator=(view_translate_single const & rhs) noexcept = default;
195 constexpr view_translate_single & operator=(view_translate_single && rhs) noexcept = default;
196 ~view_translate_single() noexcept = default;
210 if (__builtin_popcount(
static_cast<uint8_t
>(_tf)) > 1)
224 template <
typename rng_t>
227 std::ranges::viewable_range<rng_t> &&
228 std::constructible_from<urng_t, std::ranges::ref_view<std::remove_reference_t<rng_t>>>
231 : view_translate_single{
std::views::all(
std::
forward<rng_t>(_urange)), _tf}
251 iterator
begin() noexcept
257 const_iterator
begin() const noexcept
275 iterator
end() noexcept
277 return {*
this,
size()};
281 const_iterator
end() const noexcept
283 return {*
this,
size()};
324 size_type
size()
const
367 reference operator[](size_type
const n)
373 return translate_triplet((urange)[n * 3], (urange)[n * 3 + 1], (urange)[n * 3 + 2]);
379 return translate_triplet((urange)[n * 3 + 1], (urange)[n * 3 + 2], (urange)[n * 3 + 3]);
385 return translate_triplet((urange)[n * 3 + 2], (urange)[n * 3 + 3], (urange)[n * 3 + 4]);
397 const_reference operator[](size_type
const n)
const
403 return translate_triplet((urange)[n * 3], (urange)[n * 3 + 1], (urange)[n * 3 + 2]);
409 return translate_triplet((urange)[n * 3 + 1], (urange)[n * 3 + 2], (urange)[n * 3 + 3]);
415 return translate_triplet((urange)[n * 3 + 2], (urange)[n * 3 + 3], (urange)[n * 3 + 4]);
429 template <
typename urng_t>
430 view_translate_single(urng_t &&,
translation_frames const) -> view_translate_single<std::views::all_t<urng_t>>;
434 template <
typename urng_t>
435 view_translate_single(urng_t &&) -> view_translate_single<std::views::all_t<urng_t>>;
500 namespace seqan3::detail
511 template <std::ranges::view urng_t>
513 requires std::ranges::sized_range<urng_t> &&
514 std::ranges::random_access_range<urng_t> &&
517 class view_translate :
public std::ranges::view_base
525 small_vector<translation_frames, 6> selected_frames{};
532 using reference = view_translate_single<urng_t>;
534 using const_reference = reference;
536 using value_type = reference;
538 using size_type = std::ranges::range_size_t<urng_t>;
540 using difference_type = std::ranges::range_difference_t<urng_t>;
542 using iterator = detail::random_access_iterator<view_translate>;
544 using const_iterator = detail::random_access_iterator<view_translate const>;
554 template <
typename t>
555 requires (range_dimension_v<t> == range_dimension_v<value_type> + 1) &&
556 std::is_same_v<std::remove_cvref_t<range_innermost_value_t<value_type>>,
558 static constexpr
bool is_compatible_this_aux =
true;
567 view_translate() noexcept = default;
568 constexpr view_translate(view_translate const & rhs) noexcept = default;
569 constexpr view_translate(view_translate && rhs) noexcept = default;
570 constexpr view_translate & operator=(view_translate const & rhs) noexcept = default;
571 constexpr view_translate & operator=(view_translate && rhs) noexcept = default;
572 ~view_translate() noexcept = default;
599 template <
typename rng_t>
602 std::ranges::viewable_range<rng_t> &&
603 std::constructible_from<urng_t, std::ranges::ref_view<std::remove_reference_t<rng_t>>>
606 : view_translate{
std::views::all(
std::
forward<rng_t>(_urange)), _tf}
626 iterator
begin() noexcept
632 const_iterator
begin() const noexcept
650 iterator
end() noexcept
652 return {*
this,
size()};
656 const_iterator
end() const noexcept
658 return {*
this,
size()};
672 size_type
size() noexcept
674 return (size_type) selected_frames.size();
678 size_type
size() const noexcept
680 return (size_type) selected_frames.size();
701 reference operator[](size_type
const n)
708 const_reference operator[](size_type
const n)
const
717 template <
typename urng_t>
719 requires std::ranges::sized_range<urng_t> &&
720 std::ranges::random_access_range<urng_t> &&
Provides seqan3::aa27, container aliases and string literals.
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:102
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:53
auto operator|(validator1_type &&vali1, validator2_type &&vali2)
Enables the chaining of validators.
Definition: validators.hpp:1037
constexpr auto complement
Return the complement of a nucleotide object.
Definition: concept.hpp:95
@ single
The text is a single range.
Definition: concept.hpp:84
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:116
constexpr auto translate
A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames.
Definition: translate.hpp:780
constexpr auto translate_single
A view that translates nucleotide into aminoacid alphabet for one of the six frames.
Definition: translate.hpp:492
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:68
A concept that indicates whether an alphabet represents nucleotides.
The SeqAn namespace for views.
Definition: view_iota_simd.hpp:218
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
constexpr bool add_enum_bitwise_operators< translation_frames >
Enable bitwise operators for enum translation_frames.
Definition: translate.hpp:82
translation_frames
Specialisation values for single and multiple translation frames.
Definition: translate.hpp:65
@ FWD_REV_0
The first forward and first reverse frame.
@ REV_FRAME_0
The first reverse frame starting at position 0.
@ REV_FRAME_1
The second reverse frame starting at position 1.
@ FWD_REV_2
The first third and third reverse frame.
@ FWD_FRAME_2
The third forward frame starting at position 2.
@ FWD_FRAME_1
The second forward frame starting at position 1.
@ REV_FRAME_2
The third reverse frame starting at position 2.
@ FWD_FRAME_0
The first forward frame starting at position 0.
@ FWD_REV_1
The second forward and second reverse frame.
SeqAn specific customisations in the standard namespace.
typename remove_cvref< t >::type remove_cvref_t
Return the input type with const, volatile and references removed (transformation_trait shortcut).
Definition: type_traits:56
Provides the seqan3::detail::random_access_iterator class.
Adaptations of concepts from the standard library.
Provides various transformation traits used by the range module.
Adaptations of concepts from the Ranges TS.
A constexpr string implementation to manipulate string literals at compile time.
Provides functions for translating a triplet of nucleotides into an amino acid.