From 7ece39f8ccf85ed2f95f0cf7cfe86693f7002bcc Mon Sep 17 00:00:00 2001 From: smehringer Date: Tue, 18 Aug 2020 07:45:33 +0200 Subject: [PATCH] [no ci] Apply changes to documentation Co-authored-by: Marcel --- doc/tutorial/pairwise_alignment/index.md | 12 ++++++------ include/seqan3/alignment/all.hpp | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/doc/tutorial/pairwise_alignment/index.md b/doc/tutorial/pairwise_alignment/index.md index 60fb51de3e4..958c404ee97 100644 --- a/doc/tutorial/pairwise_alignment/index.md +++ b/doc/tutorial/pairwise_alignment/index.md @@ -111,15 +111,15 @@ seqan3::align_cfg::method_global. It would be wrong for us to assume what the intended default behaviour should be. The global alignment can be further refined by initialising the configuration element with -the free end gap specifiers. They specify whether or not gaps at the end of the sequences are penalised. +the free end gap specifiers. They specify whether gaps at the end of the sequences are penalised. In SeqAn you can configure this behaviour for every end, namely for leading and trailing gaps of the first and second sequence. seqan3::align_cfg::method_global is constructed with 4 free end gap specifiers (one for every end): - - seqan3::align_cfg::free_end_gaps_sequence1_leading - If set to true, aligning leading gaps in first sequence is not penelised. - - seqan3::align_cfg::free_end_gaps_sequence2_leading - If set to true, aligning leading gaps in second sequence is not penelised. - - seqan3::align_cfg::free_end_gaps_sequence1_trailing - If set to true, aligning trailing gaps in first sequence is not penelised. - - seqan3::align_cfg::free_end_gaps_sequence2_trailing - If set to true, aligning trailing gaps in second sequence is not penelised. + - seqan3::align_cfg::free_end_gaps_sequence1_leading - If set to true, aligning leading gaps in first sequence is not penalised. + - seqan3::align_cfg::free_end_gaps_sequence2_leading - If set to true, aligning leading gaps in second sequence is not penalised. + - seqan3::align_cfg::free_end_gaps_sequence1_trailing - If set to true, aligning trailing gaps in first sequence is not penalised. + - seqan3::align_cfg::free_end_gaps_sequence2_trailing - If set to true, aligning trailing gaps in second sequence is not penalised. The following code snippet demonstrates the different use cases: @@ -281,7 +281,7 @@ The `edit_scheme` still has to be combined with an alignment method. When combin with the seqan3::align_cfg::method_global configuration element, the edit distance algorithm can be further refined with free end gaps (see section `Global and semi-global alignment`). -\attention Only the the following free end gap configurations are supported for the +\attention Only the following free end gap configurations are supported for the 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 diff --git a/include/seqan3/alignment/all.hpp b/include/seqan3/alignment/all.hpp index 77a212e551b..508d76f5db9 100644 --- a/include/seqan3/alignment/all.hpp +++ b/include/seqan3/alignment/all.hpp @@ -88,7 +88,7 @@ * | \ref seqan3::align_cfg::parallel "5: Parallel" | ✅ | ✅ | ✅ | ✅ | ✅ | ❌ | ✅ | ✅ | ✅ | * | \ref seqan3::align_cfg::result "6: Result" | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ❌ | ✅ | ✅ | * | \ref seqan3::align_cfg::scoring "7: Scoring scheme" | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ❌ | ✅ | - * | \ref seqan3::align_cfg::vectorised "8: Vectorised" | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ❌ | + * | \ref seqan3::align_cfg::vectorised "8: Vectorised" | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ❌ | * * \if DEV * There is an additional configuration element \ref seqan3::align_cfg::debug "Debug", which enables the output of the