[MISC] automatic linting

seqan · Jul 16, 2024 · 0f0ec94 · 0f0ec94
1 parent 11564cb
commit 0f0ec94
Show file tree

Hide file tree

Showing 3 changed files with 19 additions and 20 deletions.
diff --git a/include/seqan3/alignment/pairwise/alignment_algorithm.hpp b/include/seqan3/alignment/pairwise/alignment_algorithm.hpp
@@ -618,7 +618,8 @@ class alignment_algorithm :
             res.end_positions = alignment_coordinate_t{column_index_type{this->alignment_state.optimum.column_index},
                                                        row_index_type{this->alignment_state.optimum.row_index}};
             // At some point this needs to be refactored so that it is not necessary to adapt the coordinate.
-            if constexpr (traits_t::is_banded) {
+            if constexpr (traits_t::is_banded)
+            {
                 res.end_positions.second += res.end_positions.first - this->trace_matrix.band_col_index;
                 res.end_positions.first = this->to_original_sequence1_position(res.end_positions.first);
                 res.end_positions.second = this->to_original_sequence2_position(res.end_positions.second);

diff --git a/include/seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp b/include/seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp
@@ -140,9 +140,8 @@ class alignment_matrix_policy
     * band starts in the origin and ends in the sink.
     */
     template <typename sequence1_t, typename sequence2_t>
-    constexpr auto slice_sequences(sequence1_t & sequence1,
-                                   sequence2_t & sequence2,
-                                   align_cfg::band_fixed_size const & band) noexcept
+    constexpr auto
+    slice_sequences(sequence1_t & sequence1, sequence2_t & sequence2, align_cfg::band_fixed_size const & band) noexcept
     {
         size_t seq1_size = std::ranges::distance(sequence1);
         size_t seq2_size = std::ranges::distance(sequence2);
@@ -200,7 +199,8 @@ class alignment_matrix_policy
      *
      * Only changes the position if the sequence was sliced due to band configuration.
      */
-    constexpr size_t to_original_sequence1_position(size_t position) const noexcept {
+    constexpr size_t to_original_sequence1_position(size_t position) const noexcept
+    {
         return position + seq1_slice_offset;
     }
 
@@ -212,7 +212,8 @@ class alignment_matrix_policy
      *
      * Only changes the position if the sequence was sliced due to band configuration.
      */
-    constexpr size_t to_original_sequence2_position(size_t position) const noexcept {
+    constexpr size_t to_original_sequence2_position(size_t position) const noexcept
+    {
         return position + seq2_slice_offset;
     }
 

diff --git a/test/unit/alignment/pairwise/global_affine_banded_test.cpp b/test/unit/alignment/pairwise/global_affine_banded_test.cpp
@@ -5,7 +5,6 @@
 #include <gtest/gtest.h>
 
 #include <seqan3/alignment/pairwise/align_pairwise.hpp>
-
 #include <seqan3/core/debug_stream.hpp>
 
 #include "fixture/global_affine_banded.hpp"
@@ -76,22 +75,20 @@ TEST(banded_alignment_issue3266_test, wrong_begin_and_end_position)
     using namespace seqan3;
     using namespace seqan3::literals;
 
-    const auto configGeneral =
-        align_cfg::scoring_scheme{nucleotide_scoring_scheme{match_score{1}, mismatch_score{-1}}} |
-        align_cfg::gap_cost_affine{align_cfg::open_score{0}, align_cfg::extension_score{-1}} |
-         align_cfg::method_global{
-            align_cfg::free_end_gaps_sequence1_leading{true},
-            align_cfg::free_end_gaps_sequence2_leading{true},
-            align_cfg::free_end_gaps_sequence1_trailing{true},
-            align_cfg::free_end_gaps_sequence2_trailing{true}};
+    auto const configGeneral = align_cfg::scoring_scheme{nucleotide_scoring_scheme{match_score{1}, mismatch_score{-1}}}
+                             | align_cfg::gap_cost_affine{align_cfg::open_score{0}, align_cfg::extension_score{-1}}
+                             | align_cfg::method_global{align_cfg::free_end_gaps_sequence1_leading{true},
+                                                        align_cfg::free_end_gaps_sequence2_leading{true},
+                                                        align_cfg::free_end_gaps_sequence1_trailing{true},
+                                                        align_cfg::free_end_gaps_sequence2_trailing{true}};
 
-    const auto configBanded = configGeneral | align_cfg::band_fixed_size{align_cfg::lower_diagonal{-40},
-                                                                         align_cfg::upper_diagonal{-20}};
+    auto const configBanded =
+        configGeneral | align_cfg::band_fixed_size{align_cfg::lower_diagonal{-40}, align_cfg::upper_diagonal{-20}};
 
-                              //0         1         2         3         4
-                              //01234567890123456789012345678901234567890
+    //0         1         2         3         4
+    //01234567890123456789012345678901234567890
     std::pair p{"CGTCTA"_dna4, "AAACCCGGGTTTAAACCCGGGTTTCGTGTACCCCCCCCCCC"_dna4};
-                                //                      CGTCTA
+    //                      CGTCTA
 
     auto general_results = align_pairwise(p, configGeneral);
     auto general_res = *std::ranges::begin(general_results);