aligned_sequence_concept.hpp File Reference

Includes the aligned_sequence and the related insert_gap and erase_gap functions to enable stl container support. More...

#include <iomanip>
#include <tuple>
#include <range/v3/algorithm/for_each.hpp>
#include <seqan3/alignment/exception.hpp>
#include <seqan3/alphabet/gap/all.hpp>
#include <seqan3/core/concept/tuple.hpp>
#include <seqan3/core/detail/debug_stream_type.hpp>
#include <seqan3/core/type_traits/all.hpp>
#include <seqan3/range/container/concept.hpp>
#include <seqan3/range/views/slice.hpp>
#include <seqan3/range/views/to_char.hpp>
#include <seqan3/range/views/zip.hpp>
#include <seqan3/std/ranges>

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Namespaces
	seqan3
	The main SeqAn3 namespace.

Functions
template<tuple_like tuple_t, typename char_t >
debug_stream_type< char_t > &	seqan3::operator<< (debug_stream_type< char_t > &stream, tuple_t const &alignment)
	Stream operator for alignments, which are represented as tuples of aligned sequences. More...
Aligned sequence interface for containers over the seqan3::gapped alphabet
Enables containers to model seqan3::aligned_sequence if they model seqan3::sequence_container and have a value type of the seqan3::gapped alphabet.
Aligned sequence interface for ranges that have the corresponding member functions.
Enables ranges to model seqan3::aligned_sequence if they have the member functions insert_gap() and erase_gap().
template<typename range_type >
std::ranges::iterator_t< range_type >	seqan3::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::aligned_sequence::erase_gap for ranges with the corresponding member function erase_gap(first, last). More...
template<typename range_type >
std::ranges::iterator_t< range_type >	seqan3::erase_gap (range_type &rng, std::ranges::iterator_t< range_type > const pos_it)
	An implementation of seqan3::aligned_sequence::erase_gap for ranges with the corresponding member function erase_gap(it). More...
template<typename range_type >
std::ranges::iterator_t< range_type >	seqan3::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::aligned_sequence::insert_gap for ranges with the corresponding member function insert_gap(it, size). More...

Detailed Description

Includes the aligned_sequence and the related insert_gap and erase_gap functions to enable stl container support.

Author

Svenja Mehringer <svenja.mehringer AT fu-berlin.de>