diff --git a/doc/tutorial/pairwise_alignment/configurations.cpp b/doc/tutorial/pairwise_alignment/configurations.cpp index 11980a0a94..2481da8e41 100644 --- a/doc/tutorial/pairwise_alignment/configurations.cpp +++ b/doc/tutorial/pairwise_alignment/configurations.cpp @@ -35,7 +35,7 @@ int main() { //! [method_global_free_end_gaps] // Example of a semi-global alignment where leading and trailing gaps in the - // second sequence are not penelised: + // second sequence are not penalised: auto config = seqan3::align_cfg::method_global{ seqan3::align_cfg::free_end_gaps_sequence1_leading{false}, seqan3::align_cfg::free_end_gaps_sequence2_leading{true}, diff --git a/doc/tutorial/pairwise_alignment/index.md b/doc/tutorial/pairwise_alignment/index.md index 767e5a9a3d..b29f5a7508 100644 --- a/doc/tutorial/pairwise_alignment/index.md +++ b/doc/tutorial/pairwise_alignment/index.md @@ -174,7 +174,7 @@ the alignment computation. The default initialised seqan3::align_cfg::gap_cost_a and for a gap opening to `0`. Note that the gap open score is added to the gap score when a gap is opened within the alignment computation. Therefore setting the gap open score to `0` disables affine gaps. You can pass a seqan3::align_cfg::extension_score and a seqan3::align_cfg::open_score object to initialise the scheme -with custom gap penalties. The penalties can be assessed changed later by using the respective member variables +with custom gap penalties. The penalties can be assessed changed later by using the respective member variables `extension_score` and `open_score`. \attention SeqAn's alignment algorithm computes the maximal similarity score, thus the match score must be set to a @@ -296,17 +296,16 @@ global alignment configuration with the edit scheme: - no free end gaps (all free end gap specifiers are set to `false`) - free end gaps for the first sequence (free end gaps are set to `true` for the first and to `false` for the second sequence) -Using any other free end gap configuration will -disable the edit distance and fall back to the standard pairwise alignment and will not use the fast bitvector -algorithm. +Using any other free end gap configuration will disable the edit distance and fall back to the standard pairwise +alignment and will not use the fast bitvector algorithm. ### Refine edit distance -The edit distance can be further refined using the seqan3::align_cfg::min_score configuration to fix an edit score (a limit of the allowed number of edits).. If the -respective alignment could not find a solution within the given error bound, the resulting score is infinity -(corresponds to std::numeric_limits::max). Also the alignment and the begin and end positions of the alignment can be -computed using a combination of the align_cfg::output_alignment, align_cfg::output_begin_position and -align_cfg::output_end_position options. +The edit distance can be further refined using the seqan3::align_cfg::min_score configuration to fix an edit score +(a limit of the allowed number of edits).. If the respective alignment could not find a solution within the given error +bound, the resulting score is infinity (corresponds to std::numeric_limits::max). Also the alignment and the begin and +end positions of the alignment can be computed using a combination of the align_cfg::output_alignment, +align_cfg::output_begin_position and align_cfg::output_end_position options. \assignment{Assignment 6}