29template <
template <
typename...>
typename container_type,
typename seq_alph_t,
typename... rest_t>
32 -> container_type<seq_alph_t, rest_t...>;
35template <
template <
typename...>
typename container_type,
36 template <
typename...>
37 typename allocator_type,
43 -> container_type<seq_alph_t, allocator_type<seq_alph_t>, rest_t...>;
64struct unaligned_seq<t>
216 &&
requires (t v, detail::unaligned_seq_t<t> unaligned) {
220 } -> std::same_as<std::ranges::iterator_t<t>>;
223 } -> std::same_as<std::ranges::iterator_t<t>>;
226 } -> std::same_as<std::ranges::iterator_t<t>>;
229 } -> std::same_as<std::ranges::iterator_t<t>>;
231 assign_unaligned(v, unaligned)
232 } -> std::same_as<void>;
260template <sequence_container aligned_seq_t>
261 requires detail::is_gapped_alphabet<std::iter_value_t<aligned_seq_t>>
262inline typename aligned_seq_t::iterator
insert_gap(aligned_seq_t & aligned_seq,
263 typename aligned_seq_t::const_iterator pos_it)
284template <sequence_container aligned_seq_t>
285 requires detail::is_gapped_alphabet<std::iter_value_t<aligned_seq_t>>
286inline typename aligned_seq_t::iterator
insert_gap(aligned_seq_t & aligned_seq,
287 typename aligned_seq_t::const_iterator pos_it,
288 typename aligned_seq_t::size_type size)
312template <sequence_container aligned_seq_t>
313 requires detail::is_gapped_alphabet<std::iter_value_t<aligned_seq_t>>
314inline typename aligned_seq_t::iterator
erase_gap(aligned_seq_t & aligned_seq,
315 typename aligned_seq_t::const_iterator pos_it)
317 if (*pos_it != gap{})
318 throw gap_erase_failure(
"The position to be erased does not contain a gap.");
320 return aligned_seq.erase(pos_it);
343template <sequence_container aligned_seq_t>
344 requires detail::is_gapped_alphabet<std::iter_value_t<aligned_seq_t>>
345inline typename aligned_seq_t::iterator
erase_gap(aligned_seq_t & aligned_seq,
346 typename aligned_seq_t::const_iterator first,
347 typename aligned_seq_t::const_iterator last)
349 for (
auto it = first; it != last; ++it)
351 throw gap_erase_failure(
"The range to be erased contains at least one non-gap character.");
353 return aligned_seq.erase(first, last);
378template <sequence_container aligned_seq_t, std::ranges::forward_range unaligned_sequence_type>
379 requires detail::is_gapped_alphabet<std::iter_value_t<aligned_seq_t>>
381 std::ranges::range_reference_t<unaligned_sequence_type>>
382inline void assign_unaligned(aligned_seq_t & aligned_seq, unaligned_sequence_type && unaligned_seq)
386 tmp.resize(std::ranges::distance(unaligned_seq));
387#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
388# pragma GCC diagnostic push
389# pragma GCC diagnostic ignored "-Wstringop-overflow"
392#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
393# pragma GCC diagnostic pop
395 swap(aligned_seq, tmp);
419template <
typename range_type>
420 requires requires (range_type v) {
421 v.insert_gap(std::ranges::iterator_t<range_type>{});
422 v.insert_gap(std::ranges::iterator_t<range_type>{},
typename range_type::size_type{});
424std::ranges::iterator_t<range_type>
insert_gap(range_type & rng,
425 std::ranges::iterator_t<range_type>
const pos_it,
426 typename range_type::size_type
const size = 1)
428 return rng.insert_gap(pos_it, size);
447template <
typename range_type>
448 requires requires (range_type v) { v.erase_gap(std::ranges::iterator_t<range_type>{}); }
449std::ranges::iterator_t<range_type>
erase_gap(range_type & rng, std::ranges::iterator_t<range_type>
const pos_it)
451 return rng.erase_gap(pos_it);
472template <
typename range_type>
473 requires requires (range_type v) {
474 v.erase_gap(std::ranges::iterator_t<range_type>{}, std::ranges::iterator_t<range_type>{});
476std::ranges::iterator_t<range_type>
erase_gap(range_type & rng,
477 std::ranges::iterator_t<range_type>
const first,
478 std::ranges::iterator_t<range_type>
const last)
480 return rng.erase_gap(first, last);
491template <
typename... elems>
497template <
typename... elems>
Includes customized exception types for the alignment module .
A combined alphabet that can hold values of either of its alternatives..
Definition alphabet_variant.hpp:129
The alphabet of a gap character '-'.
Definition gap.hpp:36
aligned_seq_t::iterator insert_gap(aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it, typename aligned_seq_t::size_type size)
An implementation of seqan3::writable_aligned_sequence::insert_gap for sequence containers.
Definition aligned_sequence_concept.hpp:286
void assign_unaligned(aligned_seq_t &aligned_seq, unaligned_sequence_type &&unaligned_seq)
An implementation of seqan3::writable_aligned_sequence::assign_unaligned_sequence for sequence contai...
Definition aligned_sequence_concept.hpp:382
std::ranges::iterator_t< range_type > erase_gap(range_type &rng, std::ranges::iterator_t< range_type > const first, std::ranges::iterator_t< range_type > const last)
An implementation of seqan3::writable_aligned_sequence::erase_gap for ranges with the corresponding m...
Definition aligned_sequence_concept.hpp:476
aligned_seq_t::iterator erase_gap(aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it)
An implementation of seqan3::writable_aligned_sequence::erase_gap for sequence containers.
Definition aligned_sequence_concept.hpp:314
std::ranges::iterator_t< range_type > erase_gap(range_type &rng, std::ranges::iterator_t< range_type > const pos_it)
An implementation of seqan3::writable_aligned_sequence::erase_gap for ranges with the corresponding m...
Definition aligned_sequence_concept.hpp:449
aligned_seq_t::iterator erase_gap(aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator first, typename aligned_seq_t::const_iterator last)
An implementation of seqan3::writable_aligned_sequence::erase_gap for sequence containers.
Definition aligned_sequence_concept.hpp:345
std::ranges::iterator_t< range_type > insert_gap(range_type &rng, std::ranges::iterator_t< range_type > const pos_it, typename range_type::size_type const size=1)
An implementation of seqan3::writable_aligned_sequence::insert_gap for ranges with the corresponding ...
Definition aligned_sequence_concept.hpp:424
aligned_seq_t::iterator insert_gap(aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it)
An implementation of seqan3::writable_aligned_sequence::insert_gap for sequence containers.
Definition aligned_sequence_concept.hpp:262
The generic concept for an aligned sequence.
The (most general) container concept as defined by the standard library.
The generic concept for a (biological) sequence.
Resolves to std::is_assignable_v<t>.
The generic concept for an aligned sequence that is writable.
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
constexpr auto remove_gap_from_value_type(container_type< gapped< seq_alph_t >, rest_t... >) -> container_type< seq_alph_t, rest_t... >
Helper function to deduce the unaligned sequence type from an aligned sequence container.
typename unaligned_seq< t >::type unaligned_seq_t
Helper type that delegates to seqan3::detail::unaligned_seq::type.
Definition aligned_sequence_concept.hpp:71
constexpr bool all_model_aligned_seq
True, if each type models seqan3::aligned_sequence; false otherwise.
Definition aligned_sequence_concept.hpp:492
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
Additional non-standard concepts for ranges.
decltype(remove_gap_from_value_type(std::declval< t >())) type
The unaligned sequence type of t.
Definition aligned_sequence_concept.hpp:57
Default transformation trait that shall expose the unaligned sequence type of t when specialised.
Definition aligned_sequence_concept.hpp:48
Type that contains multiple types.
Definition type_list.hpp:26
Adaptations of concepts from the standard library.