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Merge pull request #3204 from eseiler/doc/alignment_result
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[DOC] Fix alignment_result doc
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@eseiler
eseiler authored Nov 4, 2023
2 parents 999c0bf + cb7aa56 commit 64a4313
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Showing 3 changed files with 58 additions and 30 deletions.
78 changes: 53 additions & 25 deletions include/seqan3/alignment/pairwise/alignment_result.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -49,17 +49,17 @@ template <typename sequence1_id_t,
typename trace_debug_matrix_t = std::nullopt_t *>
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.
Expand All @@ -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<std::nullopt_t *, std::nullopt_t *, std::nullopt_t *>;

//! \brief Type deduction for id and score only.
//!\brief Type deduction for id and score only.
template <typename sequence1_id_t, typename sequence2_id_t, typename score_t>
alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t)
-> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t>;

//! \brief Type deduction for id, score and end positions.
//!\brief Type deduction for id, score and end positions.
template <typename sequence1_id_t, typename sequence2_id_t, typename score_t, typename end_positions_t>
alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t)
-> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t, end_positions_t>;

//! \brief Type deduction for id, score, end positions and begin positions.
//!\brief Type deduction for id, score, end positions and begin positions.
template <typename sequence1_id_t,
typename sequence2_id_t,
typename score_t,
Expand All @@ -94,7 +94,7 @@ template <typename sequence1_id_t,
alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t)
-> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t>;

//! \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 <typename sequence1_id_t,
typename sequence2_id_t,
typename score_t,
Expand All @@ -119,7 +119,7 @@ struct alignment_result_value_type_accessor;
namespace seqan3
{

/*!\brief Stores the alignment results and gives access to score, alignment and the front and end positionss.
/*!\brief Stores the alignment results and gives access to score, alignment and the front and end positions.
* \ingroup alignment_pairwise
* \tparam alignment_result_value_t The underlying value type containing the information from the alignment computation.
*
Expand Down Expand Up @@ -147,24 +147,24 @@ template <typename alignment_result_value_t>
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);
//!\}

Expand Down Expand Up @@ -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).
Expand All @@ -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).
Expand All @@ -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
Expand All @@ -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
Expand Down
8 changes: 4 additions & 4 deletions test/documentation/DoxygenLayout.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,16 +23,16 @@
<tab type="user" visible="yes" title="Contributing" url="\ref about_contributing" intro=""/>
</tab>
<tab type="topics" visible="yes" title="API Reference" intro=""/>
<tab type="usergroup" visible="${SEQAN3_SHOW_DEV_DOCS}" title="API Reference (details)" intro="">
<tab type="usergroup" visible="yes" title="API Reference (details)" intro="">
<tab type="modules" visible="no" title="" intro="">
<tab type="modulelist" visible="yes" title="" intro=""/>
<tab type="modulemembers" visible="yes" title="" intro=""/>
</tab>
<tab type="namespaces" visible="yes" title="">
<tab type="namespacelist" visible="yes" title="" intro=""/>
<tab type="namespacemembers" visible="yes" title="" intro=""/>
<tab type="namespacemembers" visible="${SEQAN3_SHOW_DEV_DOCS}" title="" intro=""/>
</tab>
<tab type="concepts" visible="yes" title="">
<tab type="concepts" visible="${SEQAN3_SHOW_DEV_DOCS}" title="">
</tab>
<tab type="interfaces" visible="no" title="">
<tab type="interfacelist" visible="yes" title="" intro=""/>
Expand All @@ -54,7 +54,7 @@
<tab type="exceptionindex" visible="$ALPHABETICAL_INDEX" title=""/>
<tab type="exceptionhierarchy" visible="yes" title="" intro=""/>
</tab>
<tab type="files" visible="yes" title="">
<tab type="files" visible="${SEQAN3_SHOW_DEV_DOCS}" title="">
<tab type="filelist" visible="yes" title="" intro=""/>
<tab type="globals" visible="yes" title="" intro=""/>
</tab>
Expand Down
2 changes: 1 addition & 1 deletion test/documentation/seqan3_doxygen_cfg.in
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Original file line number Diff line number Diff line change
Expand Up @@ -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 =
Expand Down

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