[MISC] Move aligned_ends to align_cg::detail.

seqan · Aug 18, 2020 · e8ed941 · e8ed941
1 parent 365e905
commit e8ed941
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Showing 5 changed files with 12 additions and 11 deletions.
diff --git a/include/seqan3/alignment/configuration/align_config_aligned_ends.hpp b/include/seqan3/alignment/configuration/align_config_aligned_ends.hpp
@@ -6,7 +6,7 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Provides seqan3::align_cfg::aligned_ends.
+ * \brief Provides seqan3::align_cfg::detail::aligned_ends.
  * \author Jörg Winkler <j.winkler AT fu-berlin.de>
  * \author Rene Rahn <rene.rahn AT fu-berlin.de>
  */
@@ -512,7 +512,7 @@ inline constexpr end_gaps free_ends_second{front_end_first<std::false_type>{},
 //!\}
 } // namespace seqan3
 
-namespace seqan3::align_cfg
+namespace seqan3::align_cfg::detail
 {
 
 // ----------------------------------------------------------------------------

diff --git a/include/seqan3/alignment/configuration/detail.hpp b/include/seqan3/alignment/configuration/detail.hpp
@@ -24,7 +24,7 @@ enum struct align_config_id : uint8_t
 {
     //!\brief ID for the \ref seqan3::align_cfg::alignment_result_capture "alignment_result_capture" option.
     alignment_result_capture,
-    aligned_ends, //!< ID for the \ref seqan3::align_cfg::aligned_ends "aligned_ends" option.
+    aligned_ends, //!< ID for the \ref seqan3::align_cfg::detail::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.
     gap,          //!< ID for the \ref seqan3::align_cfg::gap "gap" option.
@@ -54,7 +54,7 @@ inline constexpr std::array<std::array<bool, static_cast<uint8_t>(align_config_i
 {
     {   //0  1  2  3  4  5  6  7  8  9 10 11 12
         { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  0: alignment_result_capture
-        { 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1}, //  1: aligned_ends
+        { 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1}, //  1: detail::aligned_ends
         { 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  2: band
         { 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  3: debug
         { 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1}, //  4: gap

diff --git a/include/seqan3/alignment/pairwise/alignment_configurator.hpp b/include/seqan3/alignment/pairwise/alignment_configurator.hpp
@@ -597,7 +597,7 @@ constexpr function_wrapper_t alignment_configurator::configure_free_ends_initial
         if constexpr (traits_t::is_global)
         {
             if (auto method_global_cfg = cfg.get_or(align_cfg::method_global{});
-                !config_t::template exists<seqan3::align_cfg::aligned_ends>() &&
+                !config_t::template exists<seqan3::detail::align_cfg::aligned_ends>() &&
                 (method_global_cfg.free_end_gaps_sequence1_leading ||
                  method_global_cfg.free_end_gaps_sequence1_trailing ||
                  method_global_cfg.free_end_gaps_sequence2_leading ||

diff --git a/include/seqan3/alignment/pairwise/detail/type_traits.hpp b/include/seqan3/alignment/pairwise/detail/type_traits.hpp
@@ -124,7 +124,7 @@ struct alignment_configuration_traits
     static constexpr bool is_global =
         configuration_t::template exists<seqan3::align_cfg::method_global>();
     //!\brief Flag indicating whether global alignment mode with free ends is enabled.
-    static constexpr bool with_free_end_gaps = configuration_t::template exists<align_cfg::aligned_ends>();
+    static constexpr bool with_free_end_gaps = configuration_t::template exists<align_cfg::detail::aligned_ends>();
     //!\brief Flag indicating whether local alignment mode is enabled.
     static constexpr bool is_local = configuration_t::template exists<seqan3::detail::method_local_tag>();
     //!\brief Flag indicating whether banded alignment mode is enabled.

diff --git a/test/snippet/alignment/configuration/align_cfg_aligned_ends.cpp b/test/snippet/alignment/configuration/align_cfg_aligned_ends.cpp
@@ -3,17 +3,18 @@
 int main()
 {
     // Setup for overlap alignment.
-    seqan3::align_cfg::aligned_ends overlap{seqan3::free_ends_all};
+    seqan3::align_cfg::detail::aligned_ends overlap{seqan3::free_ends_all};
 
     // Setup for global alignment.
-    seqan3::align_cfg::aligned_ends global{seqan3::free_ends_none};
+    seqan3::align_cfg::detail::aligned_ends global{seqan3::free_ends_none};
 
     // Setup for semi-global alignment with free-end gaps in the first sequence.
-    seqan3::align_cfg::aligned_ends semi_seq1{seqan3::free_ends_first};
+    seqan3::align_cfg::detail::aligned_ends semi_seq1{seqan3::free_ends_first};
 
     // Setup for semi-global alignment with free-end gaps in the second sequence.
-    seqan3::align_cfg::aligned_ends semi_seq2{seqan3::free_ends_second};
+    seqan3::align_cfg::detail::aligned_ends semi_seq2{seqan3::free_ends_second};
 
     // Custom settings.
-    seqan3::align_cfg::aligned_ends custom{seqan3::end_gaps{seqan3::front_end_first{std::true_type{}}, seqan3::front_end_second{std::true_type{}}}};
+    seqan3::align_cfg::detail::aligned_ends custom{
+        seqan3::end_gaps{seqan3::front_end_first{std::true_type{}}, seqan3::front_end_second{std::true_type{}}}};
 }