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 = seqan3::detail::parallel_mode< std::integral_constant< seqan3::detail::align_config_id, seqan3::detail::align_config_id::parallel > >
	Enables the parallel execution of the alignment algorithm if possible for the given configuration.

Functions
Type deduction guides
template<std::copy_constructible callback_t>
	on_result (callback_t &&) -> on_result< std::decay_t< callback_t > >
	Deduces the callback type from a forwarding constructor argument.

Variables
constexpr configuration	edit_scheme
	Shortcut for edit distance configuration.

Detailed Description

A special sub namespace for the alignment configurations.