Merge pull request #2045 from smehringer/alignment_configuration_free…

…_end_gaps_1 [Alignment Configuration] Change member variables of method_global to booleans.
seqan · Aug 25, 2020 · bd5a78e · bd5a78e
2 parents 0d96cea + 78c6942
commit bd5a78e
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Showing 2 changed files with 22 additions and 22 deletions.
diff --git a/include/seqan3/alignment/configuration/align_config_method.hpp b/include/seqan3/alignment/configuration/align_config_method.hpp
@@ -132,14 +132,14 @@ struct method_global : public pipeable_config_element<method_global>
     {}
     //!\}
 
-    //!\brief If set to `true`, leading gaps in sequence1 are not penalized when computing the optimal alignment.
-    seqan3::align_cfg::free_end_gaps_sequence1_leading free_end_gaps_sequence1_leading{false};
-    //!\brief If set to `true`, leading gaps in sequence2 are not penalized when computing the optimal alignment.
-    seqan3::align_cfg::free_end_gaps_sequence2_leading free_end_gaps_sequence2_leading{false};
-    //!\brief If set to `true`, trailing gaps in sequence1 are not penalized when computing the optimal alignment.
-    seqan3::align_cfg::free_end_gaps_sequence1_trailing free_end_gaps_sequence1_trailing{false};
-    //!\brief If set to `true`, trailing gaps in sequence2 are not penalized when computing the optimal alignment.
-    seqan3::align_cfg::free_end_gaps_sequence2_trailing free_end_gaps_sequence2_trailing{false};
+    //!\brief If set to `true`, leading gaps in sequence1 are not penalised when computing the optimal alignment.
+    bool free_end_gaps_sequence1_leading{false};
+    //!\brief If set to `true`, leading gaps in sequence2 are not penalised when computing the optimal alignment.
+    bool free_end_gaps_sequence2_leading{false};
+    //!\brief If set to `true`, trailing gaps in sequence1 are not penalised when computing the optimal alignment.
+    bool free_end_gaps_sequence1_trailing{false};
+    //!\brief If set to `true`, trailing gaps in sequence2 are not penalised when computing the optimal alignment.
+    bool free_end_gaps_sequence2_trailing{false};
 
     //!\privatesection
     //!\brief An internal id used to check for a valid alignment configuration.

diff --git a/test/unit/alignment/configuration/align_config_method_test.cpp b/test/unit/alignment/configuration/align_config_method_test.cpp
@@ -28,18 +28,18 @@ TEST(method_global, access_member_variables)
     seqan3::align_cfg::method_global opt{}; // default construction
 
     // all default to false
-    EXPECT_FALSE(opt.free_end_gaps_sequence1_leading.get());
-    EXPECT_FALSE(opt.free_end_gaps_sequence2_leading.get());
-    EXPECT_FALSE(opt.free_end_gaps_sequence1_trailing.get());
-    EXPECT_FALSE(opt.free_end_gaps_sequence2_trailing.get());
-
-    opt.free_end_gaps_sequence1_leading = seqan3::align_cfg::free_end_gaps_sequence1_leading{true};
-    opt.free_end_gaps_sequence2_leading = seqan3::align_cfg::free_end_gaps_sequence2_leading{true};
-    opt.free_end_gaps_sequence1_trailing = seqan3::align_cfg::free_end_gaps_sequence1_trailing{true};
-    opt.free_end_gaps_sequence2_trailing = seqan3::align_cfg::free_end_gaps_sequence2_trailing{true};
-
-    EXPECT_TRUE(opt.free_end_gaps_sequence1_leading.get());
-    EXPECT_TRUE(opt.free_end_gaps_sequence2_leading.get());
-    EXPECT_TRUE(opt.free_end_gaps_sequence1_trailing.get());
-    EXPECT_TRUE(opt.free_end_gaps_sequence2_trailing.get());
+    EXPECT_FALSE(opt.free_end_gaps_sequence1_leading);
+    EXPECT_FALSE(opt.free_end_gaps_sequence2_leading);
+    EXPECT_FALSE(opt.free_end_gaps_sequence1_trailing);
+    EXPECT_FALSE(opt.free_end_gaps_sequence2_trailing);
+
+    opt.free_end_gaps_sequence1_leading = true;
+    opt.free_end_gaps_sequence2_leading = true;
+    opt.free_end_gaps_sequence1_trailing = true;
+    opt.free_end_gaps_sequence2_trailing = true;
+
+    EXPECT_TRUE(opt.free_end_gaps_sequence1_leading);
+    EXPECT_TRUE(opt.free_end_gaps_sequence2_leading);
+    EXPECT_TRUE(opt.free_end_gaps_sequence1_trailing);
+    EXPECT_TRUE(opt.free_end_gaps_sequence2_trailing);
 }