[MISC] Use method_global free_end gap config in policies.

include/seqan3/alignment/pairwise/detail/policy_affine_gap_recursion.hpp

@@ -98,9 +98,9 @@ class policy_affine_gap_recursion
             gap_open_score = static_cast<score_type>(selected_gap_scheme.get_gap_open_score()) + gap_extension_score;
         }
 
-        auto align_ends_config = config.get_or(align_cfg::aligned_ends{free_ends_none}).value;
-        first_row_is_free = align_ends_config[0];
-        first_column_is_free = align_ends_config[2];
+        auto method_global_config = config.get_or(align_cfg::method_global{});
+        first_row_is_free = method_global_config.free_end_gaps_sequence1_leading;
+        first_column_is_free = method_global_config.free_end_gaps_sequence2_leading;
     }
     //!\}
 

include/seqan3/alignment/pairwise/detail/policy_alignment_matrix.hpp

@@ -100,23 +100,20 @@ class policy_alignment_matrix
 
         bool invalid_band = upper_diagonal < lower_diagonal;
         std::string error_cause = (invalid_band) ? " The upper diagonal is smaller than the lower diagonal." : "";
-        if constexpr (traits_t::with_free_end_gaps)
+
+        if constexpr (traits_t::is_global)
         {
-            auto aligned_ends_config = seqan3::get<align_cfg::aligned_ends>(config).value;
-            bool first_row_is_free = aligned_ends_config[0];
-            bool first_column_is_free = aligned_ends_config[2];
+            auto method_global_config = get<seqan3::align_cfg::method_global>(config);
+
+            bool first_row_is_free = method_global_config.free_end_gaps_sequence1_leading;
+            bool first_column_is_free = method_global_config.free_end_gaps_sequence2_leading;
 
-            last_row_is_free = aligned_ends_config[1];
-            last_column_is_free = aligned_ends_config[3];
+            last_row_is_free = method_global_config.free_end_gaps_sequence1_trailing;
+            last_column_is_free = method_global_config.free_end_gaps_sequence2_trailing;
             // band starts in first column without free gaps or band starts in first row without free gaps.
             invalid_band |= (upper_diagonal < 0 && !first_column_is_free) || (lower_diagonal > 0 && !first_row_is_free);
             error_cause += " The band starts in a region without free gaps.";
         }
-        else if constexpr (traits_t::is_global)
-        {
-            invalid_band |= (upper_diagonal < 0 || lower_diagonal > 0);
-            error_cause += " The first cell of the matrix is not enclosed by the band.";
-        }
 
         if (invalid_band)
             throw invalid_alignment_configuration{"The selected band [" + std::to_string(lower_diagonal) + ":" +
@@ -193,18 +190,14 @@ class policy_alignment_matrix
 
         bool invalid_band = false;
         std::string error_cause{};
-        if constexpr (traits_t::with_free_end_gaps)
+
+        if constexpr (traits_t::is_global)
         {
             // band ends in last column without free gaps or band ends in last row without free gaps.
             invalid_band |= (lower_diagonal_ends_behind_last_cell && !last_column_is_free) ||
                             (upper_diagonal_ends_before_last_cell && !last_row_is_free);
             error_cause = "The band ends in a region without free gaps.";
         }
-        else if constexpr (traits_t::is_global)
-        {
-            invalid_band |= (upper_diagonal_ends_before_last_cell || lower_diagonal_ends_behind_last_cell);
-            error_cause = "The last cell of the matrix is not enclosed by the band.";
-        }
 
         if (invalid_band)
             throw invalid_alignment_configuration{"The selected band [" + std::to_string(lower_diagonal) + ":" +

include/seqan3/alignment/pairwise/detail/policy_optimum_tracker.hpp

@@ -133,14 +133,14 @@ class policy_optimum_tracker
      *
      * \details
      *
-     * Reads the state of seqan3::align_cfg::aligned_ends and enables the tracking of the last row or column if
+     * Reads the state of seqan3::align_cfg::method_global and enables the tracking of the last row or column if
      * requested. Otherwise, only the last cell will be tracked.
      */
     policy_optimum_tracker(alignment_configuration_t const & config)
     {
-        auto align_ends_config = config.get_or(align_cfg::aligned_ends{free_ends_none}).value;
-        test_last_row_cell = align_ends_config[1];
-        test_last_column_cell = align_ends_config[3];
+        auto method_global_config = config.get_or(align_cfg::method_global{});
+        test_last_row_cell = method_global_config.free_end_gaps_sequence1_trailing;
+        test_last_column_cell = method_global_config.free_end_gaps_sequence2_trailing;
     }
     //!\}