Data structures and utility functions for configuring alignment algorithm. More...
Enumerations | |
enum | seqan3::free_ends_at : uint8_t { seqan3::none = 0b0000, seqan3::free_ends_at::seq1_front = 0b0001, seqan3::free_ends_at::seq1_back = 0b0010, seqan3::free_ends_at::seq2_front = 0b0100, seqan3::free_ends_at::seq2_back = 0b1000, seqan3::free_ends_at::seq1 = seq1_front | seq1_back, seqan3::free_ends_at::seq2 = seq2_front | seq2_back, seqan3::free_ends_at::all = seq1 | seq2 } |
Enum class for all supported sequence ends specifications. More... | |
enum | seqan3::align_cfg::id : uint8_t { seqan3::align_cfg::id::gap, seqan3::align_cfg::id::sequence_ends, seqan3::align_cfg::id::score, seqan3::align_cfg::id::global, seqan3::align_cfg::id::output, seqan3::align_cfg::id::max_error, seqan3::align_cfg::id::DEV } |
Specifies an id for every configuration element. More... | |
enum | seqan3::search_cfg::id : uint8_t { seqan3::search_cfg::id::max_error, max_error_rate, output, mode } |
Specifies an id for every configuration element. More... | |
Variables | |
constexpr detail::align_config_band_adaptor< seqan3::band_static > | seqan3::align_cfg::band_static |
A configuration adaptor for a static band. | |
constexpr detail::align_config_gap_adaptor< seqan3::detail::align_config_gap > | seqan3::align_cfg::gap |
A configuration adaptor for gaps. | |
constexpr detail::align_config_global_adaptor | seqan3::align_cfg::global |
A configuration adaptor for global alignment. | |
constexpr detail::align_config_max_error_adaptor | seqan3::align_cfg::max_error |
A configuration adaptor for maximal errors. | |
template<align_result_key e> | |
constexpr detail::align_config_output_adaptor< e > | seqan3::align_cfg::output |
A configuration adaptor for alignment output. | |
constexpr detail::align_config_score_adaptor | seqan3::align_cfg::score |
A configuration adaptor for alignment scoring. | |
template<free_ends_at val = free_ends_at::none> | |
constexpr detail::align_config_sequence_ends_adaptor< val > | seqan3::align_cfg::sequence_ends |
A configuration adaptor for gaps at the sequence ends. More... | |
Data structures and utility functions for configuring alignment algorithm.
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strong |
Enum class for all supported sequence ends specifications.
The members specify where continuous gaps in the beginning or end of a sequence are not penalized in the alignment.
Enumerator | |
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none | No free gaps at the sequence ends. Each gap is scored according to seqan3::align_cfg::gap. |
seq1_front | Continuous gaps in the beginning of the first sequence are not scored. |
seq1_back | Continuous gaps at the end of the first sequence are not scored. |
seq2_front | Continuous gaps in the beginning of the second sequence are not scored. |
seq2_back | Continuous gaps at the end of the second sequence are not scored. |
seq1 | Continuous gaps in the beginning and end of the first sequence are not scored. |
seq2 | Continuous gaps in the beginning and end of the second sequence are not scored. |
all | Continuous gaps in the beginning and end of both sequences are not scored. |
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strong |
Specifies an id for every configuration element.
The seqan3::align_cfg::id is used to identify a specific alignment configuration element independent of it's concrete type and position within the seqan3::align_cfg::alignment_configuration object. Thus one can access the value of the corresponding configuration element via the special get interface.
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strong |
Specifies an id for every configuration element.
The seqan3::search_cfg::id is used to identify a specific search configuration element independent of it's concrete type and position within the seqan3::search_cfg::search_configuration object. Thus one can access the value of the corresponding configuration element via the special get interface.
Enumerator | |
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max_error | Identifier for max_errors configuration. |
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inline |
A configuration adaptor for gaps at the sequence ends.
val | An enum value that specifies which sequence ends allow gaps without penalty. |
This configuration allows to specify, whether continuous gaps in the front or end of a sequence are penalized in the alignment.