Provides configuration elements for the pairwise alignment configuration. More...
Classes | |
struct | seqan3::align_cfg::aligned_ends< end_gaps_t > |
The configuration for aligned sequence ends. More... | |
struct | seqan3::back_end_first< value_t > |
The penalty configuration for aligning the back of the first sequence with a gap. More... | |
struct | seqan3::back_end_second< value_t > |
The penalty configuration for aligning the back of the second sequence with a gap. More... | |
struct | seqan3::align_cfg::band< band_t > |
Configuration element for setting the band. More... | |
class | seqan3::end_gaps< ends_t > |
Wraps the sequence end-gap specifiers and provides ordered access to the respective values. More... | |
struct | seqan3::front_end_first< value_t > |
The penalty configuration for aligning the front of the first sequence with a gap. More... | |
struct | seqan3::front_end_second< value_t > |
The penalty configuration for aligning the front of the second sequence with a gap. More... | |
struct | seqan3::align_cfg::gap< gap_scheme_t > |
A configuration element for the gap scheme. More... | |
struct | seqan3::align_cfg::max_error |
Sets the maximal errors allowed during an edit distance computation. More... | |
struct | seqan3::align_cfg::mode< mode_type > |
Sets the alignment mode. More... | |
class | seqan3::align_cfg::result< with_type > |
Sets the result of the alignment computation. More... | |
struct | seqan3::sequence_end_gap_specifier_base< value_t, _is_static, _value > |
A mixin class which can maintain a static or a dynamic bool state. More... | |
Variables | |
constexpr configuration | seqan3::align_cfg::edit |
Shortcut for edit distance configuration. More... | |
constexpr detail::global_alignment_type | seqan3::global_alignment |
Helper variable to select the global alignment. More... | |
constexpr detail::local_alignment_type | seqan3::local_alignment |
Helper variable to select the local alignment. More... | |
Provides configuration elements for the pairwise alignment configuration.
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Shortcut for edit distance configuration.
The edit distance computation is a specific sub-problem of the alignment computation with the aim to count the number of edits to transform one sequence into another. An edit operation can be a substitution, an insertion, or a deletion. Accordingly, this algorithm uses a predefined scoring scheme as well as a gap scheme, where the score for a match is 0, for a mismatch -1, for a gap -1, and for a gap open 0.
Under the hood SeqAn uses a fast bit-vector algorithm to compute the edit distance whenever possible. This depends on the final alignment configuration. Currently, the fast edit distance algorithm is only triggered for global alignments and semi-global alignments with free ends in the first sequence.
The performance of the algorithm can further be improved if the number of maximal errors (edits) is known by using the align_cfg::max_error configuration.
cfg_slow
in the above example will trigger the slower algorithm which can handle the case if the ends are free in the second sequence instead of the first sequence.
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Helper variable to select the global alignment.
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Helper variable to select the local alignment.