The configuration for aligned sequence ends. More...
#include <seqan3/alignment/configuration/align_config_aligned_ends.hpp>
Public Attributes | |
end_gaps_t | value |
The stored config value. | |
Related Functions | |
(Note that these are not member functions.) | |
Type deduction guides | |
template<typename end_gaps_t > | |
aligned_ends (end_gaps_t) -> aligned_ends< std::remove_reference_t< end_gaps_t >> | |
Deduces the end-gaps object type from the constructor argument. | |
The configuration for aligned sequence ends.
end_gaps_t | The type of the end-gaps. Must be a specialisation of seqan3::end_gaps. |
This configuration element configures the aligned ends to further refine the global alignment algorithm. Particularly, the ends of the alignment can be penalised with gap costs or not. For example, the semi-global alignment does not penalise the leading and trailing gaps of one sequence while it does for the other sequence.
The class is instantiated with an object of seqan3::end_gaps. The user can configure each of the gap specifier separately allowing for maximal flexibility when configuring the alignment algorithm. However, there are also predefined configurations which should be preferred whenever possible.
If this configuration element is not specified for the alignment algorithm, it will automatically default to free_ends_none which computes a global alignment.