[FEATURE] move align_config::debug to align_config::detail::debug

Signed-off-by: Lydia Buntrock <[email protected]>

include/seqan3/alignment/all.hpp

@@ -92,9 +92,9 @@
  * | \ref seqan3::align_cfg::vectorised "9: Vectorised"       |  ✅   |  ✅   |  ✅   |  ✅   |  ✅   |  ✅   |  ✅   |  ✅   |  ✅   |  ❌   |
  *
  * \if DEV
- * There is an additional configuration element \ref seqan3::align_cfg::debug "Debug", which enables the output of the
- * alignment matrices from the DP algorithm using the returned seqan3::alignment_result. It is compatible with all
- * other configuration elements.
+ * There is an additional configuration element \ref seqan3::align_cfg::detail::debug "Debug", which enables the output
+ * of the alignment matrices from the DP algorithm using the returned seqan3::alignment_result. It is compatible with
+ * all other configuration elements.
  * \endif
  *
  * ## Accessing the computed alignment

include/seqan3/alignment/configuration/align_config_debug.hpp

@@ -6,7 +6,7 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Provides seqan3::align_cfg::debug.
+ * \brief Provides seqan3::align_cfg::detail::debug.
  * \author Rene Rahn <rene.rahn AT fu-berlin.de>
  */
 
@@ -16,7 +16,7 @@
 #include <seqan3/core/algorithm/configuration_element_debug_mode.hpp>
 #include <seqan3/core/algorithm/pipeable_config_element.hpp>
 
-namespace seqan3::align_cfg
+namespace seqan3::align_cfg::detail
 {
 //!\cond DEV
 /*!\brief Configuration element for debugging the alignment algorithm.
@@ -35,4 +35,4 @@ namespace seqan3::align_cfg
 inline constexpr seqan3::detail::debug_mode<std::integral_constant<seqan3::detail::align_config_id,
                                                                    seqan3::detail::align_config_id::debug>> debug{};
 //!\endcond
-}  // namespace seqan3::align_cfg
+}  // namespace seqan3::align_cfg::detail

include/seqan3/alignment/configuration/align_config_gap.hpp

@@ -6,7 +6,7 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Provides seqan3::align_config::gap.
+ * \brief Provides seqan3::align_cfg::gap.
  * \author Rene Rahn <rene.rahn AT fu-berlin.de>
  * \author Jörg Winkler <j.winkler AT fu-berlin.de>
  */

include/seqan3/alignment/configuration/detail.hpp

@@ -26,7 +26,7 @@ enum struct align_config_id : uint8_t
     alignment_result_capture,
     aligned_ends, //!< ID for the \ref seqan3::align_cfg::aligned_ends "aligned_ends" option.
     band,         //!< ID for the \ref seqan3::align_cfg::band_fixed_size "band" option.
-    debug,        //!< ID for the \ref seqan3::align_cfg::debug "debug" option.
+    debug,        //!< ID for the \ref seqan3::align_cfg::detail::debug "debug" option.
     gap,          //!< ID for the \ref seqan3::align_cfg::gap "gap" option.
     global,       //!< ID for the \ref seqan3::align_cfg::method_global "global alignment" option.
     local,        //!< ID for the \ref seqan3::align_cfg::method_local "local alignment" option.

include/seqan3/alignment/pairwise/alignment_algorithm.hpp

@@ -360,8 +360,8 @@ class alignment_algorithm :
      *
      * \details
      *
-     * Initialises the debug matrices if the alignment algorithm is running in debug mode. See seqan3::align_cfg::debug
-     * for more information.
+     * Initialises the debug matrices if the alignment algorithm is running in debug mode. See
+     * seqan3::align_cfg::detail::debug for more information.
      */
     template <typename sequence1_t, typename sequence2_t>
     constexpr void initialise_debug_matrices(sequence1_t & sequence1, sequence2_t & sequence2)
@@ -586,8 +586,8 @@ class alignment_algorithm :
      * 3. The begin positions of the aligned range for the first and second sequence.
      * 4. The alignment between both sequences in the respective aligned region.
      *
-     * If the alignment is run in debug mode (see seqan3::align_cfg::debug) the debug score and optionally trace matrix
-     * are stored in the alignment result as well.
+     * If the alignment is run in debug mode (see seqan3::align_cfg::detail::debug) the debug score and optionally trace
+     * matrix are stored in the alignment result as well.
      *
      * Finally, the callback is invoked with the computed alignment result.
      */
@@ -671,8 +671,8 @@ class alignment_algorithm :
      * 3. The begin positions of the aligned range for the first and second sequence.
      * 4. The alignment between both sequences in the respective aligned region.
      *
-     * If the alignment is run in debug mode (see seqan3::align_cfg::debug) the debug score and optionally trace matrix
-     * are stored in the alignment result as well.
+     * If the alignment is run in debug mode (see seqan3::align_cfg::detail::debug) the debug score and optionally trace
+     * matrix are stored in the alignment result as well.
      *
      * Finally, the callback is invoked with each computed alignment result iteratively.
      */

include/seqan3/alignment/pairwise/alignment_configurator.hpp

@@ -482,7 +482,7 @@ struct alignment_configurator
      * \details
      *
      * The correct scoring scheme is selected based on the vectorisation mode. If no vectorisation is enabled, the
-     * scoring scheme is the one configured in seqan3::align_config::scoring. If vectorisation is enabled, then the
+     * scoring scheme is the one configured in seqan3::align_cfg::scoring. If vectorisation is enabled, then the
      * appropriate scoring scheme for the vectorised alignment algorithm is selected. This involves checking whether the
      * passed scoring scheme is a matrix or a simple scoring scheme, which has only mismatch and match costs.
      */

include/seqan3/alignment/pairwise/alignment_result.hpp

@@ -36,11 +36,11 @@ class policy_alignment_result_builder;
  *
  * \tparam id_t                  The type for the alignment identifier.
  * \tparam score_t               The type for the resulting score.
- * \tparam end_positions_t          The type for the end positions, can be omitted.
- * \tparam begin_positions_t         The type for the begin positions, can be omitted.
+ * \tparam end_positions_t       The type for the end positions, can be omitted.
+ * \tparam begin_positions_t     The type for the begin positions, can be omitted.
  * \tparam alignment_t           The type for the alignment, can be omitted.
- * \tparam score_debug_matrix_t  The type for the score matrix. Only present if seqan3::align_cfg::debug is enabled.
- * \tparam trace_debug_matrix_t  The type for the trace matrix. Only present if seqan3::align_cfg::debug is enabled.
+ * \tparam score_debug_matrix_t  The type for the score matrix. Only present if seqan3::align_cfg::detail::debug is enabled.
+ * \tparam trace_debug_matrix_t  The type for the trace matrix. Only present if seqan3::align_cfg::detail::debug is enabled.
  */
 template <typename id_t,
           typename score_t,
@@ -62,9 +62,9 @@ struct alignment_result_value_type
     //! \brief The alignment, i.e. the actual base pair matching.
     alignment_t alignment{};
 
-    //!\brief The score matrix. Only accessible with seqan3::align_cfg::debug.
+    //!\brief The score matrix. Only accessible with seqan3::align_cfg::detail::debug.
     score_debug_matrix_t score_debug_matrix{};
-    //!\brief The trace matrix. Only accessible with seqan3::align_cfg::debug.
+    //!\brief The trace matrix. Only accessible with seqan3::align_cfg::detail::debug.
     trace_debug_matrix_t trace_debug_matrix{};
 };
 
@@ -295,10 +295,10 @@ class alignment_result
      * \details
      *
      * This function is only used for debugging such that performance can be affected significantly when enabling
-     * seqan3::align_cfg::debug.
+     * seqan3::align_cfg::detail::debug.
      *
      * \note This function is only available if the debug mode was requested via the alignment configuration
-     * (see seqan3::align_cfg::debug).
+     * (see seqan3::align_cfg::detail::debug).
      */
     constexpr auto const & score_matrix() const noexcept
     {
@@ -313,10 +313,10 @@ class alignment_result
      * \details
      *
      * This function is only used for debugging such that performance can be affected significantly when enabling
-     * seqan3::align_cfg::debug.
+     * seqan3::align_cfg::detail::debug.
      *
      * \note This function is only available if the debug mode and the alignment was requested via the alignment
-     * configuration (see seqan3::align_cfg::debug and seqan3::align_cfg::result).
+     * configuration (see seqan3::align_cfg::detail::debug and seqan3::align_cfg::result).
      */
     constexpr auto const & trace_matrix() const noexcept
     {

test/unit/alignment/pairwise/pairwise_alignment_single_test_template.hpp

@@ -86,7 +86,7 @@ TYPED_TEST_P(pairwise_alignment_test, alignment)
 {
     auto const & fixture = this->fixture();
     seqan3::configuration align_cfg = fixture.config | seqan3::align_cfg::result{seqan3::with_alignment}
-                                                     | seqan3::align_cfg::debug;
+                                                     | seqan3::align_cfg::detail::debug;
 
     std::vector database = fixture.sequence1;
     std::vector query = fixture.sequence2;