seqan3::align_cfg Namespace Reference

A special sub namespace for the alignment configurations. More...

Classes
class	band_fixed_size
	Configuration element for setting a fixed size band. More...
struct	extension_score
	A strong type of underlying type int32_t that represents the score (usually negative) of any character against a gap character. More...
struct	free_end_gaps_sequence1_leading
	A strong type representing free_end_gaps_sequence1_leading of the seqan3::align_cfg::method_global. More...
struct	free_end_gaps_sequence1_trailing
	A strong type representing free_end_gaps_sequence1_trailing of the seqan3::align_cfg::method_global. More...
struct	free_end_gaps_sequence2_leading
	A strong type representing free_end_gaps_sequence2_leading of the seqan3::align_cfg::method_global. More...
struct	free_end_gaps_sequence2_trailing
	A strong type representing free_end_gaps_sequence2_trailing of the seqan3::align_cfg::method_global. More...
class	gap_cost_affine
	A configuration element for the affine gap cost scheme. More...
struct	lower_diagonal
	A strong type representing the lower diagonal of the seqan3::align_cfg::band_fixed_size. More...
class	method_global
	Sets the global alignment method. More...
class	method_local
	Sets the local alignment method. More...
class	min_score
	Sets the minimal score (maximal errors) allowed during an distance computation e.g. edit distance. More...
class	on_result
	Configuration element to provide a user defined callback function for the alignment. More...
struct	open_score
	A strong type of underlying type int32_t that represents a score (usually negative) that is incurred once per stretch of consecutive gaps. More...
class	output_alignment
	Configures the alignment result to output the alignment. More...
class	output_begin_position
	Configures the alignment result to output the begin positions. More...
class	output_end_position
	Configures the alignment result to output the end position. More...
class	output_score
	Configures the alignment result to output the score. More...
class	output_sequence1_id
	Configures the alignment result to output the id of the first sequence. More...
class	output_sequence2_id
	Configures the alignment result to output the id of the second sequence. More...
class	score_type
	A configuration element to set the score type used in the alignment algorithm. More...
class	scoring_scheme
	Sets the scoring scheme for the alignment algorithm. More...
struct	upper_diagonal
	A strong type representing the upper diagonal of the seqan3::align_cfg::band_fixed_size. More...
class	vectorised
	Enables the vectorised alignment computation if possible for the current configuration. More...

Typedefs
using	parallel
	Enables the parallel execution of the alignment algorithm if possible for the given configuration.

Variables
constexpr configuration	edit_scheme
	Shortcut for edit distance configuration.

Type deduction guides
template<std::move_constructible callback_t>
	on_result (callback_t &&) -> on_result< std::decay_t< callback_t > >
	Deduces the callback type from a forwarding constructor argument.
template<typename scheme_t>
	scoring_scheme (scheme_t) -> scoring_scheme< std::remove_cvref_t< scheme_t > >
	Deduces the scoring scheme type from the constructor argument.

Detailed Description

A special sub namespace for the alignment configurations.