From 4fdf50668388bfcb44523139ae2ae7770d003795 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Thu, 2 Nov 2023 13:37:50 +0100 Subject: [PATCH 1/3] [DOC] Fix alignment_result doc --- .../alignment/pairwise/alignment_result.hpp | 40 ++++++++++++++++--- 1 file changed, 34 insertions(+), 6 deletions(-) diff --git a/include/seqan3/alignment/pairwise/alignment_result.hpp b/include/seqan3/alignment/pairwise/alignment_result.hpp index 2bff956ea3..596eade3bb 100644 --- a/include/seqan3/alignment/pairwise/alignment_result.hpp +++ b/include/seqan3/alignment/pairwise/alignment_result.hpp @@ -233,7 +233,15 @@ class alignment_result } /*!\brief Returns the end position of the first sequence of the alignment. - * \return The calculated alignment end of sequence 1 (inclusive). + * \return The calculated alignment end of sequence 1 (exclusive). + * \details + * + * \if DEV + * The return type (default: `size_t`) is deduced from + * seqan3::detail::alignment_result_value_type::end_positions_t::first. + * \else + * The return type is `size_t`. + * \endif * * \note This function is only available if the end position of the first sequence was requested via the * alignment configuration (see seqan3::align_cfg::output_end_position). @@ -247,7 +255,15 @@ class alignment_result } /*!\brief Returns the end position of the second sequence of the alignment. - * \return A pair of positions in the respective sequences, where the calculated alignment ends (inclusive). + * \return The calculated alignment end of sequence 2 (exclusive). + * \details + * + * \if DEV + * The return type (default: `size_t`) is deduced from + * seqan3::detail::alignment_result_value_type::end_positions_t::second. + * \else + * The return type is `size_t`. + * \endif * * \note This function is only available if the end position of the second sequence was requested via the * alignment configuration (see seqan3::align_cfg::output_end_position). @@ -261,10 +277,16 @@ class alignment_result } /*!\brief Returns the begin position of the first sequence of the alignment. - * \return A pair of positions in the respective sequences, where the calculated alignment starts. - * + * \return The calculated alignment begin of sequence 1 (inclusive). * \details * + * \if DEV + * The return type (default: `size_t`) is deduced from + * seqan3::detail::alignment_result_value_type::begin_positions_t::first. + * \else + * The return type is `size_t`. + * \endif + * * Guaranteed to be smaller than or equal to `sequence1_end_position()`. * * \note This function is only available if the begin position of the first sequence was requested via the @@ -279,10 +301,16 @@ class alignment_result } /*!\brief Returns the begin position of the second sequence of the alignment. - * \return A pair of positions in the respective sequences, where the calculated alignment starts. - * + * \return The calculated alignment begin of sequence 2 (inclusive). * \details * + * \if DEV + * The return type (default: `size_t`) is deduced from + * seqan3::detail::alignment_result_value_type::begin_positions_t::second. + * \else + * The return type is `size_t`. + * \endif + * * Guaranteed to be smaller than or equal to `sequence2_end_position()`. * * \note This function is only available if the begin position of the second sequence was requested via the From ed42028bceb075c80c8b11f828a1b77c9f7ba44c Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Thu, 2 Nov 2023 14:22:10 +0100 Subject: [PATCH 2/3] [DOC] typos --- .../alignment/pairwise/alignment_result.hpp | 38 +++++++++---------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/include/seqan3/alignment/pairwise/alignment_result.hpp b/include/seqan3/alignment/pairwise/alignment_result.hpp index 596eade3bb..bed73123db 100644 --- a/include/seqan3/alignment/pairwise/alignment_result.hpp +++ b/include/seqan3/alignment/pairwise/alignment_result.hpp @@ -49,17 +49,17 @@ template struct alignment_result_value_type { - //! \brief The alignment identifier for the first sequence. + //!\brief The alignment identifier for the first sequence. sequence1_id_t sequence1_id{}; - //! \brief The alignment identifier for the second sequence. + //!\brief The alignment identifier for the second sequence. sequence2_id_t sequence2_id{}; - //! \brief The alignment score. + //!\brief The alignment score. score_t score{}; - //! \brief The end positions of the alignment. + //!\brief The end positions of the alignment. end_positions_t end_positions{}; - //! \brief The begin positions of the alignment. + //!\brief The begin positions of the alignment. begin_positions_t begin_positions{}; - //! \brief The alignment, i.e. the actual base pair matching. + //!\brief The alignment, i.e. the actual base pair matching. alignment_t alignment{}; //!\brief The score matrix. Only accessible with seqan3::align_cfg::detail::debug. @@ -72,20 +72,20 @@ struct alignment_result_value_type * \brief Type deduction for the different combinations of result types. * \{ */ -//! \brief Type deduction for an empty object. It will always fail the compilation, if any field is accessed. +//!\brief Type deduction for an empty object. It will always fail the compilation, if any field is accessed. alignment_result_value_type()->alignment_result_value_type; -//! \brief Type deduction for id and score only. +//!\brief Type deduction for id and score only. template alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t) -> alignment_result_value_type; -//! \brief Type deduction for id, score and end positions. +//!\brief Type deduction for id, score and end positions. template alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t) -> alignment_result_value_type; -//! \brief Type deduction for id, score, end positions and begin positions. +//!\brief Type deduction for id, score, end positions and begin positions. template alignment_result_value_type; -//! \brief Type deduction for id, score, end positions, begin positions and alignment. +//!\brief Type deduction for id, score, end positions, begin positions and alignment. template class alignment_result { private: - //! \brief Object that stores the computed alignment results. + //!\brief Object that stores the computed alignment results. alignment_result_value_t data{}; /*!\name Member types * \brief Local definition of the types contained in the `data` object. * \{ */ - //! \brief The type for the alignment identifier for the first sequence. + //!\brief The type for the alignment identifier for the first sequence. using sequence1_id_t = decltype(data.sequence1_id); - //! \brief The type for the alignment identifier for the second sequence. + //!\brief The type for the alignment identifier for the second sequence. using sequence2_id_t = decltype(data.sequence2_id); - //! \brief The type for the resulting score. + //!\brief The type for the resulting score. using score_t = decltype(data.score); - //! \brief The type for the end positions. + //!\brief The type for the end positions. using end_positions_t = decltype(data.end_positions); - //! \brief The type for the begin positions. + //!\brief The type for the begin positions. using begin_positions_t = decltype(data.begin_positions); - //! \brief The type for the alignment. + //!\brief The type for the alignment. using alignment_t = decltype(data.alignment); //!\} From cb7aa568616229d171a1bcf21d1c3158639630b7 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Thu, 2 Nov 2023 14:22:27 +0100 Subject: [PATCH 3/3] [DOC] Visibility issues --- test/documentation/DoxygenLayout.xml | 8 ++++---- test/documentation/seqan3_doxygen_cfg.in | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/test/documentation/DoxygenLayout.xml b/test/documentation/DoxygenLayout.xml index c20d745fd4..15f74bb3a2 100644 --- a/test/documentation/DoxygenLayout.xml +++ b/test/documentation/DoxygenLayout.xml @@ -23,16 +23,16 @@ - + - + - + @@ -54,7 +54,7 @@ - + diff --git a/test/documentation/seqan3_doxygen_cfg.in b/test/documentation/seqan3_doxygen_cfg.in index 5d893ad7d1..dbd11fce7d 100644 --- a/test/documentation/seqan3_doxygen_cfg.in +++ b/test/documentation/seqan3_doxygen_cfg.in @@ -123,7 +123,7 @@ ENABLED_SECTIONS = ${SEQAN3_DOXYGEN_ENABLED_SECTIONS} MAX_INITIALIZER_LINES = 30 SHOW_USED_FILES = YES SHOW_FILES = YES -SHOW_NAMESPACES = ${SEQAN3_SHOW_DEV_DOCS} +SHOW_NAMESPACES = YES FILE_VERSION_FILTER = LAYOUT_FILE = ${SEQAN3_DOXYGEN_OUTPUT_DIR}/DoxygenLayout.xml CITE_BIB_FILES =