A configuration element for the gap scheme. More...
#include <seqan3/alignment/configuration/align_config_gap.hpp>
Public Attributes | |
gap_scheme_t | value |
The stored config value. | |
Related Functions | |
(Note that these are not member functions.) | |
Type deduction guides | |
template<typename scheme_t > | |
gap (scheme_t) -> gap< scheme_t > | |
Deduces the gap scheme from the constructor argument. | |
A configuration element for the gap scheme.
gap_scheme_t | The type of the underlying gap scheme; must be of type seqan3::gap_scheme. |
Configures the gap scheme for the alignment algorithm. The gap scheme determines how gaps are penalised inside of the alignment algorithm. If the gap scheme is not configured, it will default to a linear gap scheme initialised with edit distance. Note that the gap open score is used as an additional score. This means that the score for opening a gap during the affine alignment execution is the sum of the gap score and the gap open score.