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domainWorld
BioSeqDataLib
Commits
524c63f5
Commit
524c63f5
authored
Mar 01, 2018
by
Carsten Kemena
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[AlignmentMatrix] added gop/gep return function
parent
3aa6e839
Changes
2
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2 changed files
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35 additions
and
0 deletions
+35
-0
src/align/AlignmentMatrix.hpp
src/align/AlignmentMatrix.hpp
+23
-0
tests/align/AlignmentMatrix_Test.hpp
tests/align/AlignmentMatrix_Test.hpp
+12
-0
No files found.
src/align/AlignmentMatrix.hpp
View file @
524c63f5
...
...
@@ -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
View file @
524c63f5
...
...
@@ -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"
);
...
...
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