33 namespace seqan3::detail
36 template <std::ranges::view urng_t>
38 requires std::ranges::sized_range<urng_t> &&
39 std::ranges::random_access_range<urng_t> &&
44 template <std::ranges::view urng_t>
46 requires std::ranges::sized_range<urng_t> &&
47 std::ranges::random_access_range<urng_t> &&
50 class view_translate_single;
82 #ifdef SEQAN3_DEPRECATED_310
102 constexpr
bool add_enum_bitwise_operators<translation_frames> =
true;
107 namespace seqan3::detail
117 template <
bool single>
128 return detail::adaptor_from_functor{*
this, tf};
136 template <std::ranges::range urng_t>
137 constexpr
auto operator()(urng_t && urange,
translation_frames const tf = default_frames)
const
139 static_assert(std::ranges::viewable_range<urng_t>,
140 "The range parameter to views::translate[_single] cannot be a temporary of a non-view range.");
141 static_assert(std::ranges::sized_range<urng_t>,
142 "The range parameter to views::translate[_single] must model std::ranges::sized_range.");
143 static_assert(std::ranges::random_access_range<urng_t>,
144 "The range parameter to views::translate[_single] must model std::ranges::random_access_range.");
146 "The range parameter to views::translate[_single] must be over elements of seqan3::nucleotide_alphabet.");
149 return detail::view_translate_single{std::forward<urng_t>(urange), tf};
151 return detail::view_translate{std::forward<urng_t>(urange), tf};
155 template <std::ranges::range urng_t>
156 constexpr
friend auto operator|(urng_t && urange, translate_fn
const & me)
158 return me(std::forward<urng_t>(urange));
172 template <std::ranges::view urng_t>
174 requires std::ranges::sized_range<urng_t> &&
175 std::ranges::random_access_range<urng_t> &&
178 class view_translate_single :
public std::ranges::view_base
186 static constexpr small_string multiple_frame_error{
"Error: Invalid type of frame. Choose one out of "
187 "forward_frame0, reverse_frame0, forward_frame1, "
188 "reverse_frame1, forward_frame2 and reverse_frame2."};
194 using reference = aa27;
196 using const_reference = aa27;
198 using value_type = aa27;
200 using size_type = std::ranges::range_size_t<urng_t>;
202 using difference_type = std::ranges::range_difference_t<urng_t>;
204 using iterator = detail::random_access_iterator<view_translate_single>;
206 using const_iterator = detail::random_access_iterator<view_translate_single const>;
212 view_translate_single() noexcept = default;
213 constexpr view_translate_single(view_translate_single const & rhs) noexcept = default;
214 constexpr view_translate_single(view_translate_single && rhs) noexcept = default;
215 constexpr view_translate_single & operator=(view_translate_single const & rhs) noexcept = default;
216 constexpr view_translate_single & operator=(view_translate_single && rhs) noexcept = default;
217 ~view_translate_single() noexcept = default;
231 if (__builtin_popcount(
static_cast<uint8_t
>(_tf)) > 1)
245 template <
typename rng_t>
248 std::ranges::viewable_range<rng_t> &&
249 std::constructible_from<urng_t, std::ranges::ref_view<std::remove_reference_t<rng_t>>>
252 : view_translate_single{
std::views::all(
std::
forward<rng_t>(_urange)), _tf}
272 iterator
begin() noexcept
278 const_iterator
begin() const noexcept
296 iterator
end() noexcept
298 return {*
this,
size()};
302 const_iterator
end() const noexcept
304 return {*
this,
size()};
345 size_type
size()
const
388 reference operator[](size_type
const n)
400 return translate_triplet((urange)[n * 3], (urange)[n * 3 + 1], (urange)[n * 3 + 2]);
408 return translate_triplet((urange)[n * 3 + 1], (urange)[n * 3 + 2], (urange)[n * 3 + 3]);
416 return translate_triplet((urange)[n * 3 + 2], (urange)[n * 3 + 3], (urange)[n * 3 + 4]);
430 const_reference operator[](size_type
const n)
const
442 return translate_triplet((urange)[n * 3], (urange)[n * 3 + 1], (urange)[n * 3 + 2]);
450 return translate_triplet((urange)[n * 3 + 1], (urange)[n * 3 + 2], (urange)[n * 3 + 3]);
458 return translate_triplet((urange)[n * 3 + 2], (urange)[n * 3 + 3], (urange)[n * 3 + 4]);
474 template <
typename urng_t>
475 view_translate_single(urng_t &&,
translation_frames const) -> view_translate_single<std::views::all_t<urng_t>>;
479 template <
typename urng_t>
480 view_translate_single(urng_t &&) -> view_translate_single<std::views::all_t<urng_t>>;
547 namespace seqan3::detail
558 template <std::ranges::view urng_t>
560 requires std::ranges::sized_range<urng_t> &&
561 std::ranges::random_access_range<urng_t> &&
564 class view_translate :
public std::ranges::view_base
572 small_vector<translation_frames, 6> selected_frames{};
579 using reference = view_translate_single<urng_t>;
581 using const_reference = reference;
583 using value_type = reference;
585 using size_type = std::ranges::range_size_t<urng_t>;
587 using difference_type = std::ranges::range_difference_t<urng_t>;
589 using iterator = detail::random_access_iterator<view_translate>;
591 using const_iterator = detail::random_access_iterator<view_translate const>;
602 template <
typename t>
603 requires (range_dimension_v<t> == range_dimension_v<value_type> + 1) &&
604 std::is_same_v<std::remove_cvref_t<range_innermost_value_t<value_type>>,
606 static constexpr
bool is_compatible_this_aux =
true;
615 view_translate() noexcept = default;
616 constexpr view_translate(view_translate const & rhs) noexcept = default;
617 constexpr view_translate(view_translate && rhs) noexcept = default;
618 constexpr view_translate & operator=(view_translate const & rhs) noexcept = default;
619 constexpr view_translate & operator=(view_translate && rhs) noexcept = default;
620 ~view_translate() noexcept = default;
647 template <
typename rng_t>
650 std::ranges::viewable_range<rng_t> &&
651 std::constructible_from<urng_t, std::ranges::ref_view<std::remove_reference_t<rng_t>>>
654 : view_translate{
std::views::all(
std::
forward<rng_t>(_urange)), _tf}
658 #ifdef SEQAN3_DEPRECATED_310
659 template <
typename rng_t>
662 std::ranges::viewable_range<rng_t> &&
663 std::constructible_from<urng_t, std::ranges::ref_view<std::remove_reference_t<rng_t>>>
665 view_translate(rng_t && _urange)
687 iterator
begin() noexcept
693 const_iterator
begin() const noexcept
711 iterator
end() noexcept
713 return {*
this,
size()};
717 const_iterator
end() const noexcept
719 return {*
this,
size()};
733 size_type
size() noexcept
735 return (size_type) selected_frames.size();
739 size_type
size() const noexcept
741 return (size_type) selected_frames.size();
762 reference operator[](size_type
const n)
769 const_reference operator[](size_type
const n)
const
780 #ifdef SEQAN3_DEPRECATED_310
781 template <
typename urng_t>
783 requires std::ranges::sized_range<urng_t> &&
784 std::ranges::random_access_range<urng_t> &&
787 view_translate (urng_t &&) -> view_translate<std::views::all_t<urng_t>>;
791 template <
typename urng_t>
793 requires std::ranges::sized_range<urng_t> &&
794 std::ranges::random_access_range<urng_t> &&
797 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::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:1103
constexpr auto complement
Return the complement of a nucleotide object.
Definition: concept.hpp:104
@ single
The text is a single range.
Definition: concept.hpp:83
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:151
constexpr auto translate
A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames.
Definition: translate.hpp:859
constexpr auto translate_single
A view that translates nucleotide into aminoacid alphabet for one of the six frames.
Definition: translate.hpp:539
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
A concept that indicates whether an alphabet represents nucleotides.
The SeqAn namespace for views.
Definition: char_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:68
@ 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.
SeqAn specific customisations in the standard namespace.
Adaptations of concepts from the Ranges TS.
Provides functions for translating a triplet of nucleotides into an amino acid.
A constexpr string implementation to manipulate string literals at compile time.
Provides seqan3::views::deep.