SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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The default traits type for the edit distance algorithm. More...
#include <seqan3/alignment/pairwise/edit_distance_fwd.hpp>
Public Types | |
using | align_config_type = std::remove_reference_t< align_config_t > |
The type of the alignment config. | |
using | alignment_result_type = typename alignment_traits_type::alignment_result_type |
The alignment result type generated by the algorithm. | |
using | alignment_traits_type = alignment_configuration_traits< align_config_type > |
The alignment algorithm traits over the alignment configuration type. | |
using | database_iterator = std::ranges::iterator_t< database_type > |
The type of an iterator of the database sequence. | |
using | database_type = std::remove_reference_t< database_t > |
The type of the database sequence. | |
using | query_alphabet_type = std::remove_reference_t< std::ranges::range_reference_t< query_type > > |
The alphabet type of the query sequence. | |
using | query_type = std::remove_reference_t< query_t > |
The type of the query sequence. | |
using | result_value_type = typename alignment_result_value_type_accessor< alignment_result_type >::type |
The alignment result value type. | |
using | score_matrix_type = edit_distance_score_matrix_full< word_type, score_type, is_semi_global, use_max_errors > |
The type of the score matrix. | |
using | score_type = typename alignment_traits_type::original_score_type |
The type of the score. | |
using | trace_matrix_type = edit_distance_trace_matrix_full< word_type, is_semi_global, use_max_errors > |
The type of the trace matrix. | |
using | word_type = word_t |
The type of one machine word. | |
Static Public Attributes | |
static constexpr bool | compute_begin_positions |
Whether the alignment configuration indicates to compute and/or store the begin positions. | |
static constexpr bool | compute_end_positions |
Whether the alignment configuration indicates to compute and/or store the end positions. | |
static constexpr bool | compute_matrix = compute_score_matrix || compute_trace_matrix |
Whether the alignment configuration indicates to compute and/or store the score or trace matrix. | |
static constexpr bool | compute_score = true |
Whether the alignment configuration indicates to compute and/or store the score. | |
static constexpr bool | compute_score_matrix = false |
Whether the alignment configuration indicates to compute and/or store the score matrix. | |
static constexpr bool | compute_sequence_alignment = alignment_traits_type::compute_sequence_alignment |
Whether the alignment configuration indicates to compute and/or store the alignment of the sequences. | |
static constexpr bool | compute_trace_matrix = compute_begin_positions || compute_sequence_alignment |
Whether the alignment configuration indicates to compute and/or store the trace matrix. | |
static constexpr bool | is_global = !is_semi_global |
Whether the alignment is a global alignment or not. | |
static constexpr bool | is_semi_global = is_semi_global_t::value |
Whether the alignment is a semi-global alignment or not. | |
static constexpr bool | use_max_errors = align_config_type::template exists<align_cfg::min_score>() |
When true the computation will use the ukkonen trick with the last active cell and bounds the error to config.max_errors. | |
static constexpr uint8_t | word_size = bits_of<word_type> |
The size of one machine word. | |
The default traits type for the edit distance algorithm.
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staticconstexpr |
Whether the alignment configuration indicates to compute and/or store the begin positions.
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staticconstexpr |
Whether the alignment configuration indicates to compute and/or store the end positions.