[AlignmentMatrix] added gop/gep return function

src/align/AlignmentMatrix.hpp

@@ -273,6 +273,17 @@ public:
         gep_ = penalty;
     }
 
+    /**
+     * @brief Returns the current gap extension penalites
+     * 
+     * @return The used gap extension pentalties.
+     */
+    DataType
+    gep() const
+    {
+        return gep_;
+    }
+
     /**
      * \brief Sets gap opening penalties.
      * @param  penalty Value of the gap costs.
@@ -283,6 +294,18 @@ public:
         gop_ = penalty;
     }
 
+
+    /**
+     * @brief Returns the current gap opening penalties
+     * 
+     * @return The used gap openeing penalties.
+     */
+    DataType
+    gop() const
+    {
+        return gop_;
+    }
+
     /**
      * \brief Sets the similarity Matrix.
      * @param  mat The matrix to use.

tests/align/AlignmentMatrix_Test.hpp

@@ -42,6 +42,18 @@
 
 BOOST_AUTO_TEST_SUITE(AlignementMatrix_Test)
 
+BOOST_AUTO_TEST_CASE( general_tests)
+{
+	BioSeqDataLib::AlignmentMatrix<float, BioSeqDataLib::SimilarityMatrix<float> > mat;
+	mat.gop(-0.5);
+	BOOST_CHECK_EQUAL(mat.gop(), -0.5);
+
+	mat.gep(-6);
+	BOOST_CHECK_EQUAL(mat.gep(), -6);
+}
+
+
+
 BOOST_AUTO_TEST_CASE( nw_sequence_test)
 {
 	BioSeqDataLib::Sequence<> seq1("seq1", "LMLDSGSEPKLIAEPLXPQGPYELSDETLQAPVLNDEGTEAVFELLSNAVEV", "", "test sequence");