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 constexpr
bool add_enum_bitwise_operators<translation_frames> =
true;
91 namespace seqan3::detail
101 template <
bool single>
112 return detail::adaptor_from_functor{*
this, tf};
120 template <std::ranges::range urng_t>
121 constexpr
auto operator()(urng_t && urange,
translation_frames const tf = default_frames)
const
123 static_assert(std::ranges::viewable_range<urng_t>,
124 "The range parameter to views::translate[_single] cannot be a temporary of a non-view range.");
125 static_assert(std::ranges::sized_range<urng_t>,
126 "The range parameter to views::translate[_single] must model std::ranges::sized_range.");
127 static_assert(std::ranges::random_access_range<urng_t>,
128 "The range parameter to views::translate[_single] must model std::ranges::random_access_range.");
130 "The range parameter to views::translate[_single] must be over elements of seqan3::nucleotide_alphabet.");
133 return detail::view_translate_single{std::forward<urng_t>(urange), tf};
135 return detail::view_translate{std::forward<urng_t>(urange), tf};
139 template <std::ranges::range urng_t>
140 constexpr
friend auto operator|(urng_t && urange, translate_fn
const & me)
142 return me(std::forward<urng_t>(urange));
156 template <std::ranges::view urng_t>
158 requires std::ranges::sized_range<urng_t> &&
159 std::ranges::random_access_range<urng_t> &&
162 class view_translate_single :
public std::ranges::view_base
170 static constexpr small_string multiple_frame_error{
"Error: Invalid type of frame. Choose one out of FWD_FRAME_0, "
171 "REV_FRAME_0, FWD_FRAME_1, REV_FRAME_1, FWD_FRAME_2 and "
178 using reference = aa27;
180 using const_reference = aa27;
182 using value_type = aa27;
184 using size_type = std::ranges::range_size_t<urng_t>;
186 using difference_type = std::ranges::range_difference_t<urng_t>;
188 using iterator = detail::random_access_iterator<view_translate_single>;
190 using const_iterator = detail::random_access_iterator<view_translate_single const>;
196 view_translate_single() noexcept = default;
197 constexpr view_translate_single(view_translate_single const & rhs) noexcept = default;
198 constexpr view_translate_single(view_translate_single && rhs) noexcept = default;
199 constexpr view_translate_single & operator=(view_translate_single const & rhs) noexcept = default;
200 constexpr view_translate_single & operator=(view_translate_single && rhs) noexcept = default;
201 ~view_translate_single() noexcept = default;
215 if (__builtin_popcount(
static_cast<uint8_t
>(_tf)) > 1)
229 template <
typename rng_t>
232 std::ranges::viewable_range<rng_t> &&
233 std::constructible_from<urng_t, std::ranges::ref_view<std::remove_reference_t<rng_t>>>
236 : view_translate_single{
std::views::all(
std::
forward<rng_t>(_urange)), _tf}
256 iterator
begin() noexcept
262 const_iterator
begin() const noexcept
280 iterator
end() noexcept
282 return {*
this,
size()};
286 const_iterator
end() const noexcept
288 return {*
this,
size()};
329 size_type
size()
const
372 reference operator[](size_type
const n)
378 return translate_triplet((urange)[n * 3], (urange)[n * 3 + 1], (urange)[n * 3 + 2]);
384 return translate_triplet((urange)[n * 3 + 1], (urange)[n * 3 + 2], (urange)[n * 3 + 3]);
390 return translate_triplet((urange)[n * 3 + 2], (urange)[n * 3 + 3], (urange)[n * 3 + 4]);
402 const_reference operator[](size_type
const n)
const
408 return translate_triplet((urange)[n * 3], (urange)[n * 3 + 1], (urange)[n * 3 + 2]);
414 return translate_triplet((urange)[n * 3 + 1], (urange)[n * 3 + 2], (urange)[n * 3 + 3]);
420 return translate_triplet((urange)[n * 3 + 2], (urange)[n * 3 + 3], (urange)[n * 3 + 4]);
434 template <
typename urng_t>
435 view_translate_single(urng_t &&,
translation_frames const) -> view_translate_single<std::views::all_t<urng_t>>;
439 template <
typename urng_t>
440 view_translate_single(urng_t &&) -> view_translate_single<std::views::all_t<urng_t>>;
505 namespace seqan3::detail
516 template <std::ranges::view urng_t>
518 requires std::ranges::sized_range<urng_t> &&
519 std::ranges::random_access_range<urng_t> &&
522 class view_translate :
public std::ranges::view_base
530 small_vector<translation_frames, 6> selected_frames{};
537 using reference = view_translate_single<urng_t>;
539 using const_reference = reference;
541 using value_type = reference;
543 using size_type = std::ranges::range_size_t<urng_t>;
545 using difference_type = std::ranges::range_difference_t<urng_t>;
547 using iterator = detail::random_access_iterator<view_translate>;
549 using const_iterator = detail::random_access_iterator<view_translate const>;
560 template <
typename t>
561 requires (range_dimension_v<t> == range_dimension_v<value_type> + 1) &&
562 std::is_same_v<std::remove_cvref_t<range_innermost_value_t<value_type>>,
564 static constexpr
bool is_compatible_this_aux =
true;
573 view_translate() noexcept = default;
574 constexpr view_translate(view_translate const & rhs) noexcept = default;
575 constexpr view_translate(view_translate && rhs) noexcept = default;
576 constexpr view_translate & operator=(view_translate const & rhs) noexcept = default;
577 constexpr view_translate & operator=(view_translate && rhs) noexcept = default;
578 ~view_translate() noexcept = default;
605 template <
typename rng_t>
608 std::ranges::viewable_range<rng_t> &&
609 std::constructible_from<urng_t, std::ranges::ref_view<std::remove_reference_t<rng_t>>>
612 : view_translate{
std::views::all(
std::
forward<rng_t>(_urange)), _tf}
632 iterator
begin() noexcept
638 const_iterator
begin() const noexcept
656 iterator
end() noexcept
658 return {*
this,
size()};
662 const_iterator
end() const noexcept
664 return {*
this,
size()};
678 size_type
size() noexcept
680 return (size_type) selected_frames.size();
684 size_type
size() const noexcept
686 return (size_type) selected_frames.size();
707 reference operator[](size_type
const n)
714 const_reference operator[](size_type
const n)
const
723 template <
typename urng_t>
725 requires std::ranges::sized_range<urng_t> &&
726 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 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
auto operator|(validator1_type &&vali1, validator2_type &&vali2)
Enables the chaining of validators.
Definition: validators.hpp:1093
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:150
constexpr auto translate
A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames.
Definition: translate.hpp:786
constexpr auto translate_single
A view that translates nucleotide into aminoacid alphabet for one of the six frames.
Definition: translate.hpp:497
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:70
A concept that indicates whether an alphabet represents nucleotides.
The SeqAn namespace for views.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
translation_frames
Specialisation values for single and multiple translation frames.
Definition: translate.hpp:67
@ 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.
Provides the seqan3::detail::random_access_iterator class.
Adaptations of concepts from the standard library.
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.