74template <std::ranges::viewable_range inner_type>
75 requires std::ranges::random_access_range<inner_type> && std::ranges::sized_range<inner_type>
76 && (std::is_const_v<std::remove_reference_t<inner_type>> || std::ranges::view<inner_type>)
81 template <
bool = true>
120 using size_type = std::ranges::range_size_t<inner_type>;
156 template <
typename other_range_t>
157 requires (!std::same_as<other_range_t, gap_decorator>)
159 && std::ranges::viewable_range<other_range_t>
181 return anchors.rbegin()->second + ungapped_view.size();
183 return ungapped_view.size();
207 assert(pos <= size());
211 if (it_set == anchors.begin())
213 anchors.emplace_hint(anchors.begin(),
anchor_gap_t{pos, count});
218 auto gap_len{it_set->second};
219 if (it_set != anchors.begin())
220 gap_len -= (*(
std::prev(it_set))).second;
222 if (it_set->first + gap_len >= pos)
225 it_set = anchors.erase(it_set);
226 anchors.insert(it_set,
gap);
232 anchors.insert(it_set,
gap);
258 throw gap_erase_failure(
"The range to be erased does not correspond to a consecutive gap.");
284 if (it == anchors.begin())
289 size_type const gap_len = gap_length(it);
292 if ((it->first + gap_len) < pos2)
294 throw gap_erase_failure{
"The range to be erased does not correspond to a consecutive gap."};
297 else if (gap_len == pos2 - pos1)
299 it = anchors.erase(it);
305 it = anchors.erase(it);
306 it = anchors.insert(it,
gap);
311 update(it, pos2 - pos1);
323 template <
typename unaligned_sequence_t>
324 requires std::assignable_from<gap_decorator &, unaligned_sequence_t>
407 throw std::out_of_range{
"Trying to access element behind the last in gap_decorator."};
415 throw std::out_of_range{
"Trying to access element behind the last in gap_decorator."};
477 return !(lhs == rhs);
486 auto lit = lhs.
begin();
487 auto rit = rhs.
begin();
489 while (lit != lhs.
end() && rit != rhs.
end() && *lit == *rit)
492 if (rit == rhs.
end())
494 else if (lit == lhs.
end())
506 auto lit = lhs.
begin();
507 auto rit = rhs.
begin();
509 while (lit != lhs.
end() && rit != rhs.
end() && *lit == *rit)
512 if (lit == lhs.
end())
514 else if (rit == rhs.
end())
526 return !(lhs <= rhs);
566 return (it == anchors.begin()) ? it->second : it->second - (*
std::prev(it)).second;
583 for (
auto it =
std::prev(anchors.end(), 1); it->first > pos;)
586 anchors.erase(*it--);
604 while (it != anchors.end())
607 it = anchors.erase(it);
608 it = anchors.insert(it,
gap);
627template <std::ranges::viewable_range urng_t>
628 requires (!std::ranges::view<std::remove_reference_t<urng_t>>)
635template <std::ranges::view urng_t>
655template <std::ranges::viewable_range inner_type>
656 requires std::ranges::random_access_range<inner_type> && std::ranges::sized_range<inner_type>
657 && (std::is_const_v<std::remove_reference_t<inner_type>> || std::ranges::view<inner_type>)
667 int64_t ungapped_view_pos{0};
675 bool is_at_gap{
true};
680 assert(new_pos <= host->size());
683 anchor_set_it = host->anchors.upper_bound(
anchor_gap_t{pos, host->bound_dummy});
684 ungapped_view_pos = pos;
686 if (anchor_set_it != host->anchors.begin())
691 if (prev != host->anchors.begin())
694 ungapped_view_pos -= prev->second;
695 left_gap_end = prev->first + gap_len;
698 if (ungapped_view_pos !=
static_cast<int64_t
>(host->ungapped_view.size()) && pos >= left_gap_end
699 && (anchor_set_it == host->anchors.end() || pos < anchor_set_it->first))
737 left_gap_end = anchor_set_it->second;
762 if (pos < left_gap_end)
765 if (anchor_set_it == host->anchors.end() || pos < anchor_set_it->first)
768 if (ungapped_view_pos !=
static_cast<int64_t
>(host->ungapped_view.size()))
773 left_gap_end = anchor_set_it->first + anchor_set_it->second
774 - ((anchor_set_it != host->anchors.begin()) ? (
std::prev(anchor_set_it))->second : 0);
778 if (left_gap_end == host->size())
796 this->jump(this->pos + skip);
818 if (pos < left_gap_end)
820 (anchor_set_it != host->anchors.begin()) ? --anchor_set_it : anchor_set_it;
822 if (anchor_set_it != host->anchors.begin())
826 prev->first + prev->second - ((prev != host->anchors.begin()) ?
std::prev(prev)->second : 0);
834 else if (anchor_set_it == host->anchors.end() || pos < anchor_set_it->first)
855 this->jump(this->pos - skip);
902 return lhs.pos == rhs.pos;
908 return lhs.pos != rhs.pos;
914 return lhs.pos < rhs.pos;
920 return lhs.pos > rhs.pos;
926 return lhs.pos <= rhs.pos;
932 return lhs.pos >= rhs.pos;
Includes customized exception types for the alignment module .
Core alphabet concept and free function/type trait wrappers.
A combined alphabet that can hold values of either of its alternatives..
Definition alphabet_variant.hpp:129
The iterator type over a seqan3::gap_decorator.
Definition gap_decorator.hpp:660
void jump(typename gap_decorator::size_type const new_pos)
A helper function that performs the random access into the anchor set, updating all member variables.
Definition gap_decorator.hpp:678
basic_iterator()=default
Defaulted.
friend bool operator<(basic_iterator const &lhs, basic_iterator const &rhs) noexcept
Checks whether *this is less than rhs.
Definition gap_decorator.hpp:912
basic_iterator & operator++()
Increments iterator.
Definition gap_decorator.hpp:757
typename gap_decorator::const_reference reference
The reference type.
Definition gap_decorator.hpp:714
friend basic_iterator operator-(difference_type const skip, basic_iterator const &it)
Returns an iterator copy advanced by skip many positions.
Definition gap_decorator.hpp:866
typename gap_decorator::value_type value_type
The value type.
Definition gap_decorator.hpp:712
basic_iterator & operator=(basic_iterator const &)=default
Defaulted.
basic_iterator(gap_decorator const &host_, typename gap_decorator::size_type const pos_)
Construct from seqan3::gap_decorator and explicit position.
Definition gap_decorator.hpp:747
basic_iterator operator--(int)
Returns a decremented iterator copy.
Definition gap_decorator.hpp:845
basic_iterator(basic_iterator const &)=default
Defaulted.
friend bool operator>=(basic_iterator const &lhs, basic_iterator const &rhs) noexcept
Checks whether *this is greater than or equal to rhs.
Definition gap_decorator.hpp:930
friend bool operator<=(basic_iterator const &lhs, basic_iterator const &rhs) noexcept
Checks whether *this is less than or equal to rhs.
Definition gap_decorator.hpp:924
reference operator*() const
Dereference operator returns a copy of the element currently pointed at.
Definition gap_decorator.hpp:882
reference operator[](difference_type const n) const
Return underlying container value currently pointed at.
Definition gap_decorator.hpp:888
friend bool operator>(basic_iterator const &lhs, basic_iterator const &rhs) noexcept
Checks whether *this is greater than rhs.
Definition gap_decorator.hpp:918
basic_iterator operator+(difference_type const skip) const
Returns an iterator copy advanced by skip many positions.
Definition gap_decorator.hpp:801
basic_iterator operator++(int)
Returns an incremented iterator copy.
Definition gap_decorator.hpp:786
~basic_iterator()=default
Defaulted.
basic_iterator operator-(difference_type const skip) const
Returns an iterator copy advanced by skip many positions.
Definition gap_decorator.hpp:860
value_type * pointer
The pointer type.
Definition gap_decorator.hpp:716
friend basic_iterator operator+(difference_type const skip, basic_iterator const &it)
Returns an iterator copy advanced by skip many positions.
Definition gap_decorator.hpp:807
basic_iterator & operator=(basic_iterator &&)=default
Defaulted.
friend bool operator==(basic_iterator const &lhs, basic_iterator const &rhs) noexcept
Checks whether *this is equal to rhs.
Definition gap_decorator.hpp:900
basic_iterator & operator+=(difference_type const skip)
Advances iterator by skip many positions.
Definition gap_decorator.hpp:794
basic_iterator(gap_decorator const &host_)
Construct from seqan3::gap_decorator and initialising to first position.
Definition gap_decorator.hpp:732
basic_iterator(basic_iterator &&)=default
Defaulted.
basic_iterator & operator--()
Decrements iterator.
Definition gap_decorator.hpp:813
typename gap_decorator::difference_type difference_type
The difference type.
Definition gap_decorator.hpp:710
basic_iterator & operator-=(difference_type const skip)
Advances iterator by skip many positions.
Definition gap_decorator.hpp:853
difference_type operator-(basic_iterator const lhs) const noexcept
Returns the distance between two iterators.
Definition gap_decorator.hpp:872
friend bool operator!=(basic_iterator const &lhs, basic_iterator const &rhs) noexcept
Checks whether *this is not equal to rhs.
Definition gap_decorator.hpp:906
A gap decorator allows the annotation of sequences with gap symbols while leaving the underlying sequ...
Definition gap_decorator.hpp:78
reference at(size_type const i)
Return the i-th element as a reference.
Definition gap_decorator.hpp:404
friend bool operator==(gap_decorator const &lhs, gap_decorator const &rhs)
Checks whether lhs is equal to rhs.
Definition gap_decorator.hpp:460
friend void assign_unaligned(gap_decorator &dec, unaligned_sequence_t &&unaligned)
Assigns a new sequence of type seqan3::gap_decorator::unaligned_sequence_type to the decorator.
Definition gap_decorator.hpp:325
typename anchor_set_type::iterator set_iterator_type
The iterator type for an anchor set.
Definition gap_decorator.hpp:547
gap_decorator & operator=(gap_decorator const &)=default
Defaulted.
gap_decorator(gap_decorator &&rhs)=default
Defaulted.
const_reference at(size_type const i) const
Return the i-th element as a reference.
Definition gap_decorator.hpp:412
std::ranges::range_difference_t< inner_type > difference_type
The difference type of the underlying sequence.
Definition gap_decorator.hpp:126
const_iterator cend() const noexcept
Returns an iterator pointing behind the last element of the decorator.
Definition gap_decorator.hpp:381
const_iterator end() const noexcept
Returns an iterator pointing behind the last element of the decorator.
Definition gap_decorator.hpp:375
typename std::pair< size_t, size_t > anchor_gap_t
The gap type as a tuple storing position and accumulated gap lengths.
Definition gap_decorator.hpp:541
void rupdate(size_type const pos, size_type const offset)
Update all anchor gaps after the indicated position by adding an offset.
Definition gap_decorator.hpp:581
inner_type unaligned_sequence_type
The underlying ungapped range type.
Definition gap_decorator.hpp:133
reference operator[](size_type const i) const
Return the i-th element as a reference.
Definition gap_decorator.hpp:431
friend bool operator!=(gap_decorator const &lhs, gap_decorator const &rhs)
Checks whether lhs is not equal to rhs.
Definition gap_decorator.hpp:475
iterator erase_gap(const_iterator const it)
Erase one gap symbol at the indicated iterator postion.
Definition gap_decorator.hpp:254
gap_decorator(other_range_t &&range)
Construct with the ungapped range type.
Definition gap_decorator.hpp:160
const_iterator begin() const noexcept
Returns an iterator to the first element of the container.
Definition gap_decorator.hpp:349
iterator insert_gap(const_iterator const it, size_type const count=1)
Insert a gap of length count at the aligned sequence iterator position.
Definition gap_decorator.hpp:201
~gap_decorator()=default
Defaulted.
iterator erase_gap(const_iterator const first, const_iterator const last)
Erase gap symbols at the iterator postions [first, last[.
Definition gap_decorator.hpp:278
gap_decorator(gap_decorator const &)=default
Defaulted.
friend bool operator<=(gap_decorator const &lhs, gap_decorator const &rhs)
Checks whether lhs is less than or equal to rhs.
Definition gap_decorator.hpp:504
size_type size() const
Returns the total length of the aligned sequence.
Definition gap_decorator.hpp:178
size_type gap_length(set_iterator_type it) const
Helper function to compute the length of the gap indicated by the input iterator.
Definition gap_decorator.hpp:564
reference const_reference
const_reference type equals reference type equals value type because the underlying sequence must not...
Definition gap_decorator.hpp:114
void update(set_iterator_type it, size_type const offset)
Update all anchor gaps after indicated position by substracting an offset.
Definition gap_decorator.hpp:602
gap_decorator & operator=(gap_decorator &&rhs)=default
Defaulted.
gapped< std::ranges::range_value_t< inner_type > > value_type
The variant type of the alphabet type and gap symbol type (see seqan3::gapped).
Definition gap_decorator.hpp:101
friend bool operator>(gap_decorator const &lhs, gap_decorator const &rhs)
Checks whether lhs is greater than rhs.
Definition gap_decorator.hpp:524
friend bool operator>=(gap_decorator const &lhs, gap_decorator const &rhs)
Checks whether lhs is greater than or equal to rhs.
Definition gap_decorator.hpp:533
gap_decorator()=default
Default constructor.
decltype(views::type_reduce(std::declval< inner_type && >())) ungapped_view_type
The type of the underlying view wrapped in seqan3::views::type_reduce.
Definition gap_decorator.hpp:91
friend bool operator<(gap_decorator const &lhs, gap_decorator const &rhs)
Checks whether lhs is less than rhs.
Definition gap_decorator.hpp:484
anchor_set_type anchors
Set storing the anchor gaps.
Definition gap_decorator.hpp:617
std::ranges::range_size_t< inner_type > size_type
The size_type of the underlying sequence.
Definition gap_decorator.hpp:120
ungapped_view_type ungapped_view
Stores a (copy of a) view to the ungapped, underlying sequence.
Definition gap_decorator.hpp:614
const_iterator cbegin() const noexcept
Returns an iterator to the first element of the container.
Definition gap_decorator.hpp:355
Thrown in function seqan3::erase_gap, if a position does not contain a gap.
Definition alignment/exception.hpp:21
The alphabet of a gap character '-'.
Definition gap.hpp:36
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
constexpr auto type_reduce
A view adaptor that behaves like std::views::all, but type erases certain ranges.
Definition type_reduce.hpp:147
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
Provides seqan3::views::type_reduce.