From 856a6e3fd1060780de48aa55d6130451d9fcba26 Mon Sep 17 00:00:00 2001 From: Kathrin Trappe Date: Mon, 16 Dec 2013 19:40:31 +0100 Subject: [PATCH 1/2] [Docs] class_G* adapted to match dev2 docu --- core/include/seqan/align/gap_anchor.h | 12 ++++++------ core/include/seqan/align/gaps_base.h | 2 +- core/include/seqan/seq_io/genomic_region.h | 2 +- core/include/seqan/stream/stream_gz_file.h | 2 ++ .../include/seqan/journaled_set/journaled_set_base.h | 2 +- 5 files changed, 11 insertions(+), 9 deletions(-) diff --git a/core/include/seqan/align/gap_anchor.h b/core/include/seqan/align/gap_anchor.h index 7e82f38d9b..76d5c89446 100644 --- a/core/include/seqan/align/gap_anchor.h +++ b/core/include/seqan/align/gap_anchor.h @@ -65,8 +65,8 @@ typedef Tag const SortGapPos; * @headerfile * @brief Stores the position of an alignment character in sequence-space and in gap-space. * - * @signature template - * struct GapAnchor; + * @signature template + * struct GapAnchor; * * @tparam TPos Type to store gapped/ungapped positions. * @@ -106,14 +106,14 @@ template struct GapAnchor { /*! - * @var VariableType GapAnchor::seqPos - * @brief Sequence character position in the ungapped sequence. + * @var TPos GapAnchor::seqPos + * @brief Sequence character position in the ungapped sequence (e.g. @link IntegerConcept @endlink). */ TPos seqPos; // sequence character position in the ungapped sequence /*! - * @var VariableType GapAnchor::gapPos - * @brief Sequence character position in the gapped sequence. + * @var TPos GapAnchor::gapPos + * @brief Sequence character position in the gapped sequence (e.g. @link IntegerConcept @endlink). */ TPos gapPos; // sequence character position in the gapped sequence diff --git a/core/include/seqan/align/gaps_base.h b/core/include/seqan/align/gaps_base.h index 4d17b78b4d..62ea74abf3 100644 --- a/core/include/seqan/align/gaps_base.h +++ b/core/include/seqan/align/gaps_base.h @@ -78,7 +78,7 @@ typedef Tag ArrayGaps; * @brief Store the gapped version of a sequence. * * @signature template - * class Gaps; + * class Gaps; * * @tparam TSequence The type of the underlying sequence. * @tparam TSpec Tag for specialization. diff --git a/core/include/seqan/seq_io/genomic_region.h b/core/include/seqan/seq_io/genomic_region.h index 6dbbbf290f..087f42742e 100644 --- a/core/include/seqan/seq_io/genomic_region.h +++ b/core/include/seqan/seq_io/genomic_region.h @@ -111,7 +111,7 @@ inline bool parse(GenomicRegion & region, CharString const & regionString); */ /*! - * @var CharString GenomicRegion::seqName; + * @var CharString GenomicRegion::seqName; * @brief Name of the sequence the region lies on, default is the empty string. * * @var __int32 GenomicRegion::seqId; diff --git a/core/include/seqan/stream/stream_gz_file.h b/core/include/seqan/stream/stream_gz_file.h index 83eb971739..f0501fafc7 100644 --- a/core/include/seqan/stream/stream_gz_file.h +++ b/core/include/seqan/stream/stream_gz_file.h @@ -55,6 +55,8 @@ inline void close(Stream & stream); /*! * @class GzFileStream + * @extends Stream + * @extends StreamConcept * @headerfile * @brief Allows to open gzip-compressed files. * @signature template <> diff --git a/extras/include/seqan/journaled_set/journaled_set_base.h b/extras/include/seqan/journaled_set/journaled_set_base.h index 1739404da6..71509566ae 100644 --- a/extras/include/seqan/journaled_set/journaled_set_base.h +++ b/extras/include/seqan/journaled_set/journaled_set_base.h @@ -205,7 +205,7 @@ struct GlobalAlign{}; * * @section Remarks * - * The JournaledManhattan strategy fills the gaps between the anchors with a single insertion node whil the + * The JournaledManhatten strategy fills the gaps between the anchors with a single insertion node whil the * corresponding part of the reference sequence is deleted. */ From 8ab60c5e5b71b5fa6308a8bbc30e3e991f87cad0 Mon Sep 17 00:00:00 2001 From: Kathrin Trappe Date: Fri, 20 Dec 2013 22:17:14 +0100 Subject: [PATCH 2/2] [Docs] class_G* adapted to match dev2 docu corrected version --- core/include/seqan/seq_io/genomic_region.h | 2 +- extras/include/seqan/journaled_set/journaled_set_base.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/core/include/seqan/seq_io/genomic_region.h b/core/include/seqan/seq_io/genomic_region.h index 087f42742e..6dbbbf290f 100644 --- a/core/include/seqan/seq_io/genomic_region.h +++ b/core/include/seqan/seq_io/genomic_region.h @@ -111,7 +111,7 @@ inline bool parse(GenomicRegion & region, CharString const & regionString); */ /*! - * @var CharString GenomicRegion::seqName; + * @var CharString GenomicRegion::seqName; * @brief Name of the sequence the region lies on, default is the empty string. * * @var __int32 GenomicRegion::seqId; diff --git a/extras/include/seqan/journaled_set/journaled_set_base.h b/extras/include/seqan/journaled_set/journaled_set_base.h index 71509566ae..1739404da6 100644 --- a/extras/include/seqan/journaled_set/journaled_set_base.h +++ b/extras/include/seqan/journaled_set/journaled_set_base.h @@ -205,7 +205,7 @@ struct GlobalAlign{}; * * @section Remarks * - * The JournaledManhatten strategy fills the gaps between the anchors with a single insertion node whil the + * The JournaledManhattan strategy fills the gaps between the anchors with a single insertion node whil the * corresponding part of the reference sequence is deleted. */