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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.

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