Commit 78d53f95 authored by Carsten Kemena's avatar Carsten Kemena

removed RASPODOM until sure that it is correct

parent 172e680c
......@@ -7,9 +7,9 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
add_compile_options(-std=c++11)
project (BioSeqDataLib_TESTS CXX)
SET(MAJOR_VERSION 1)
SET(MINOR_VERSION 0)
SET(PATCH_VERSION 0)
SET(MAJOR_VERSION 0)
SET(MINOR_VERSION 9)
SET(PATCH_VERSION 9)
SET(CMAKE_CXX_FLAGS_COVERAGE
"-g -O0 --coverage -fprofile-arcs -ftest-coverage -fno-inline -fno-inline-small-functions -fno-default-inline -pedantic -Wall -Wextra" # -Wcast-align -Wcast-qual -Wctor-dtor-privacy -Wdisabled-optimization -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wsign-conversion -Wsign-promo -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Werror -Wno-unused"
......
......@@ -144,11 +144,11 @@ private:
traceback_gotoh_() const;
/**
/*
* \brief Calculates the traceback for the Raspodom alignment
*/
*
void
traceback_raspodom_() const;
traceback_raspodom_() const;*/
/**
* \brief Calculates the traceback for the Smith-Waterman alignment
......@@ -157,7 +157,7 @@ private:
traceback_sw_() const;
using MatchTracker = std::set<std::pair<size_t, size_t> >;
/*
bool
traceback_raspodom_optimal_path_(MatchTracker &matches_tl, MatchTracker &matches_tr,
MatchTracker &matches_bl, MatchTracker &matches_br) const;
......@@ -165,7 +165,7 @@ private:
std::pair<bool, bool>
traceback_raspodom_suboptimal_path_(size_t x, size_t y, MatchTracker &matches_tl, MatchTracker &matches_tr,
MatchTracker &matches_bl, MatchTracker &matches_br) const;
*/
/**
* \brief performs a traceback
......@@ -180,9 +180,9 @@ private:
case Algorithm::Gotoh:
traceback_gotoh_();
break;
case Algorithm::Raspodom:
traceback_raspodom_();
break;
//case Algorithm::Raspodom:
// traceback_raspodom_();
// break;
case Algorithm::SW:
traceback_sw_();
break;
......@@ -253,16 +253,16 @@ public:
void
sw(const SeqType &seq1, const SeqType &seq2);
/**
/*
* \brief Run the RASPDOM algorithm
* @param seq1 First sequence
* @param seq2 Second sequence
*/
*
template<typename SeqType>
void
raspodom(const SeqType &seq1, const SeqType &seq2);
*/
/**
* \brief Sets the gap extension penalites, used as well as homogenous gap costs.
* @param penalty Value of the gap costs.
......@@ -655,7 +655,7 @@ AlignmentMatrix<DataType, SimMat>::traceback_gotoh_() const
/***************************************************
* RASPDOM - Algorithm *
***************************************************/
/*
template<typename DataType, typename SimMat>
template<typename SeqType>
void
......@@ -977,7 +977,7 @@ AlignmentMatrix<DataType, SimMat>::traceback_raspodom_() const
isCP_ = true;
}
*/
/***************************************************
* SW - Algorithm *
***************************************************/
......
......@@ -246,7 +246,7 @@ BOOST_AUTO_TEST_CASE(sw_align_test )
BOOST_CHECK_EQUAL_COLLECTIONS(result.eS2.begin(), result.eS2.end(), expected2.begin(), expected2.end());
}
/*
BOOST_AUTO_TEST_CASE(raspodom_align_domain_test )
{
......@@ -356,7 +356,7 @@ BOOST_AUTO_TEST_CASE(raspodom_align_domain_test )
BOOST_CHECK_EQUAL(mat.isCP(), false);
}
*/
BOOST_AUTO_TEST_SUITE_END()
#endif /* ALIGNMENTMATRIX_TEST_HPP_ */
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