The generic concept for an aligned sequence.This concept describes the requirements a sequence must fulfil in order to be part of the seqan3::alignment object.
More...
#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>
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(Note that these are not member functions.)
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You can expect these functions on all types that model seqan3::aligned_sequence_concept.
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seq_type::iterator | insert_gap (seq_type &seq, typename seq_type::const_iterator pos_it) |
| Insert a seqan3::gap into an aligned sequence. More...
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seq_type::iterator | insert_gap (seq_type &seq, typename seq_type::const_iterator pos_it, typename seq_type::size_type size) |
| Insert multiple seqan3::gap into an aligned sequence. More...
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seq_type::iterator | erase_gap (seq_type &seq, typename seq_type::const_iterator pos_it) |
| Erase a seqan3::gap from an aligned sequence. More...
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seq_type::iterator | erase_gap (seq_type &seq, typename seq_type::const_iterator first, typename seq_type::const_iterator last) |
| Erase multiple seqan3::gap from an aligned sequence. More...
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Enables containers to model seqan3::aligned_sequence_concept if they model seqan3::sequence_container_concept and have a reference type assignable from seqan3::gap (e.g. std::vector<seqan3::gapped<seqan3::dna4>>).
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template<sequence_container_concept seq_type> |
seq_type::iterator | insert_gap (seq_type &seq, typename seq_type::const_iterator pos_it) |
| An implementation of seqan3::aligned_sequence_concept::insert_gap for sequence containers. More...
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template<sequence_container_concept seq_type> |
seq_type::iterator | insert_gap (seq_type &seq, typename seq_type::const_iterator pos_it, typename seq_type::size_type size) |
| An implementation of seqan3::aligned_sequence_concept::insert_gap for sequence containers. More...
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template<sequence_container_concept seq_type> |
seq_type::iterator | erase_gap (seq_type &seq, typename seq_type::const_iterator pos_it) |
| An implementation of seqan3::aligned_sequence_concept::erase_gap for sequence containers. More...
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template<sequence_container_concept seq_type> |
seq_type::iterator | erase_gap (seq_type &seq, typename seq_type::const_iterator first, typename seq_type::const_iterator last) |
| An implementation of seqan3::aligned_sequence_concept::erase_gap for sequence containers. More...
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The generic concept for an aligned sequence.
This concept describes the requirements a sequence must fulfil in order to be part of the seqan3::alignment object.
The following extended type requirements for a type T
must hold true:
Concepts and doxygen
The requirements for this concept are given as related functions and metafunctions. Types that model this concept are shown as "implementing this interface".
◆ erase_gap() [1/4]
seq_type::iterator erase_gap |
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seq_type & |
seq, |
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typename seq_type::const_iterator |
pos_it |
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) |
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related |
Erase a seqan3::gap from an aligned sequence.
- Template Parameters
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- Parameters
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[in,out] | seq | The aligned sequence to modify. |
[in] | pos_it | The iterator pointing to the position where to erase a gap. |
- Exceptions
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- Attention
- This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).
◆ erase_gap() [2/4]
seq_type::iterator erase_gap |
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seq_type & |
seq, |
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typename seq_type::const_iterator |
first, |
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typename seq_type::const_iterator |
last |
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) |
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related |
Erase multiple seqan3::gap from an aligned sequence.
- Template Parameters
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- Parameters
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[in,out] | seq | The aligned sequence to modify. |
[in] | first | The iterator pointing to the position where to start erasing gaps. |
[in] | last | The iterator pointing to the position where to stop erasing gaps. |
- Exceptions
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- Attention
- This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).
◆ erase_gap() [3/4]
template<sequence_container_concept seq_type>
seq_type::iterator erase_gap |
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seq_type & |
seq, |
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typename seq_type::const_iterator |
pos_it |
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) |
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related |
An implementation of seqan3::aligned_sequence_concept::erase_gap for sequence containers.
- Template Parameters
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- Parameters
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[in,out] | seq | The container to modify. |
[in] | pos_it | The iterator pointing to the position where to erase a gap. |
- Exceptions
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This function delegates to the member function erase(iterator)
of the container. Before delegating, the function checks if the position pointed to by pos_it
is an actual seqan3::gap and throws an exception if not.
◆ erase_gap() [4/4]
template<sequence_container_concept seq_type>
seq_type::iterator erase_gap |
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seq_type & |
seq, |
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typename seq_type::const_iterator |
first, |
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typename seq_type::const_iterator |
last |
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) |
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related |
An implementation of seqan3::aligned_sequence_concept::erase_gap for sequence containers.
- Template Parameters
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- Parameters
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[in,out] | seq | The container to modify. |
[in] | first | The iterator pointing to the position where to start erasing gaps. |
[in] | last | The iterator pointing to the position where to stop erasing gaps. |
- Exceptions
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This function delegates to the member function erase(iterator, iterator)
of the container. Before delegating, the function checks if the range [first
, last
) contains only seqan3::gap symbols.
◆ insert_gap() [1/4]
seq_type::iterator insert_gap |
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seq_type & |
seq, |
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typename seq_type::const_iterator |
pos_it |
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) |
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related |
Insert a seqan3::gap into an aligned sequence.
- Template Parameters
-
- Parameters
-
[in,out] | seq | The aligned sequence to modify. |
[in] | pos_it | The iterator pointing to the position where to insert a gap. |
- Attention
- This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).
◆ insert_gap() [2/4]
seq_type::iterator insert_gap |
( |
seq_type & |
seq, |
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typename seq_type::const_iterator |
pos_it, |
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typename seq_type::size_type |
size |
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) |
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related |
Insert multiple seqan3::gap into an aligned sequence.
- Template Parameters
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- Parameters
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[in,out] | seq | The aligned sequence to modify. |
[in] | pos_it | The iterator pointing to the position where to insert a gaps. |
[in] | size | The number of gap symbols to insert (will result in a gap of length size ). |
- Attention
- This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).
◆ insert_gap() [3/4]
template<sequence_container_concept seq_type>
seq_type::iterator insert_gap |
( |
seq_type & |
seq, |
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typename seq_type::const_iterator |
pos_it |
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) |
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related |
An implementation of seqan3::aligned_sequence_concept::insert_gap for sequence containers.
- Template Parameters
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- Parameters
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[in,out] | seq | The container to modify. |
[in] | pos_it | The iterator pointing to the position where to insert a gap. |
This function delegates to the member function insert(iterator, value)
of the container.
◆ insert_gap() [4/4]
template<sequence_container_concept seq_type>
seq_type::iterator insert_gap |
( |
seq_type & |
seq, |
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typename seq_type::const_iterator |
pos_it, |
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typename seq_type::size_type |
size |
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) |
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related |
An implementation of seqan3::aligned_sequence_concept::insert_gap for sequence containers.
- Template Parameters
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- Parameters
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[in,out] | seq | The container to modify. |
[in] | pos_it | The iterator pointing to the position where to insert gaps. |
[in] | size | The number of gap symbols to insert (will result in a gap of length size ). |
This function delegates to the member function insert(iterator,
size,
value)
of the container.
The documentation for this interface was generated from the following file: