[DOC] Fix alignment_result doc

include/seqan3/alignment/pairwise/alignment_result.hpp

@@ -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.
@@ -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,
@@ -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,
@@ -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.
  *
@@ -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);
     //!\}
 
@@ -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

test/documentation/DoxygenLayout.xml

@@ -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="${SEQAN3_SHOW_DEV_DOCS}" title="">
       </tab>
       <tab type="interfaces" visible="no" title="">
         <tab type="interfacelist" visible="yes" title="" intro=""/>
@@ -54,7 +54,7 @@
         <tab type="exceptionindex" visible="$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>

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         =