seqan3::align_cfg::gap< gap_scheme_t > Struct Template Reference

A configuration element for the gap scheme. More...

#include <seqan3/alignment/configuration/align_config_gap.hpp>

Inheritance diagram for seqan3::align_cfg::gap< gap_scheme_t >:

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.

Detailed Description

template<typename gap_scheme_t>
struct seqan3::align_cfg::gap< gap_scheme_t >

A configuration element for the gap scheme.

Template Parameters

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.

Example

    using namespace seqan3;

    // Configuration with linear gaps.
    align_cfg::gap linear_cfg{gap_scheme{gap_score{-1}}};

    // Configuration with affine_gaps. Score for opening a gap during the alignment algorithm will be -11.
    align_cfg::gap affine_cfg{gap_scheme{gap_score{-1}, gap_open_score{-10}}};

See also

seqan3::gap_scheme

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The documentation for this struct was generated from the following file:

• seqan3/alignment/configuration/align_config_gap.hpp