Home
last modified time | relevance | path

Searched refs:pssm_input (Results 1 – 14 of 14) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dmsa2pssm_unit_test.cpp55 auto_ptr<CPsiBlastInputClustalW> pssm_input; in BOOST_AUTO_TEST_CASE() local
70 CPsiBlastInputClustalW pssm_input(in, *opts); in BOOST_AUTO_TEST_CASE() local
71 pssm_input.Process(); in BOOST_AUTO_TEST_CASE()
73 PSIMsa* msa = pssm_input.GetData(); in BOOST_AUTO_TEST_CASE()
102 pssm_input.Process(); in BOOST_AUTO_TEST_CASE()
104 PSIMsa* msa = pssm_input.GetData(); in BOOST_AUTO_TEST_CASE()
109 for (TSeqPos i = 0; i < pssm_input.GetQueryLength(); i++) { in BOOST_AUTO_TEST_CASE()
124 CPsiBlastInputClustalW pssm_input(in, *opts); in BOOST_AUTO_TEST_CASE() local
126 string(pssm_input.GetMatrixName())); in BOOST_AUTO_TEST_CASE()
127 pssm_input.Process(); in BOOST_AUTO_TEST_CASE()
[all …]
H A Dpssmcreate_cdd_unit_test.cpp282 CPssmInputWithSingleCD pssm_input; in BOOST_AUTO_TEST_CASE() local
328 CPssmInputWithTwoCDs pssm_input; in BOOST_AUTO_TEST_CASE() local
376 CPssmInputWithNoCDs pssm_input; in BOOST_AUTO_TEST_CASE() local
406 CPssmInputWithGapsInQuery pssm_input; in BOOST_AUTO_TEST_CASE() local
408 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
417 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
425 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
433 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
440 CPssmInputWithSingleCD pssm_input; in BOOST_AUTO_TEST_CASE() local
536 pssm_input->Process(); in BOOST_AUTO_TEST_CASE()
[all …]
H A Dpssmcreate_unit_test.cpp668 auto_ptr<CPsiBlastInputData> pssm_input( in BOOST_AUTO_TEST_CASE() local
673 CPssmEngine pssm_engine(pssm_input.get()); in BOOST_AUTO_TEST_CASE()
674 pssm_input->Process(); in BOOST_AUTO_TEST_CASE()
763 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
775 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
788 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
802 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
807 CPssmEngine pssm_engine(pssm_input.get()); in BOOST_AUTO_TEST_CASE()
868 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
878 (_PSIPackedMsaNew(pssm_input->GetData())); in BOOST_AUTO_TEST_CASE()
[all …]
H A Dpssmenginefreqratios_unit_test.cpp87 auto_ptr<IPssmInputFreqRatios> pssm_input; in BOOST_AUTO_TEST_CASE() local
88 pssm_input.reset(new CPsiBlastInputFreqRatios in BOOST_AUTO_TEST_CASE()
90 CPssmEngine pssm_engine(pssm_input.get()); in BOOST_AUTO_TEST_CASE()
110 pssm_input->GetQuery()[i], j); in BOOST_AUTO_TEST_CASE()
133 CPsiBlastInputClustalW pssm_input(in, *opts, "BLOSUM62", diags); in BOOST_AUTO_TEST_CASE() local
134 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dmsa2pssm_unit_test.cpp55 auto_ptr<CPsiBlastInputClustalW> pssm_input; in BOOST_AUTO_TEST_CASE() local
70 CPsiBlastInputClustalW pssm_input(in, *opts); in BOOST_AUTO_TEST_CASE() local
71 pssm_input.Process(); in BOOST_AUTO_TEST_CASE()
73 PSIMsa* msa = pssm_input.GetData(); in BOOST_AUTO_TEST_CASE()
102 pssm_input.Process(); in BOOST_AUTO_TEST_CASE()
104 PSIMsa* msa = pssm_input.GetData(); in BOOST_AUTO_TEST_CASE()
109 for (TSeqPos i = 0; i < pssm_input.GetQueryLength(); i++) { in BOOST_AUTO_TEST_CASE()
124 CPsiBlastInputClustalW pssm_input(in, *opts); in BOOST_AUTO_TEST_CASE() local
126 string(pssm_input.GetMatrixName())); in BOOST_AUTO_TEST_CASE()
127 pssm_input.Process(); in BOOST_AUTO_TEST_CASE()
[all …]
H A Dpssmcreate_cdd_unit_test.cpp282 CPssmInputWithSingleCD pssm_input; in BOOST_AUTO_TEST_CASE() local
328 CPssmInputWithTwoCDs pssm_input; in BOOST_AUTO_TEST_CASE() local
376 CPssmInputWithNoCDs pssm_input; in BOOST_AUTO_TEST_CASE() local
406 CPssmInputWithGapsInQuery pssm_input; in BOOST_AUTO_TEST_CASE() local
408 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
417 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
425 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
433 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
440 CPssmInputWithSingleCD pssm_input; in BOOST_AUTO_TEST_CASE() local
536 pssm_input->Process(); in BOOST_AUTO_TEST_CASE()
[all …]
H A Dpssmcreate_unit_test.cpp668 auto_ptr<CPsiBlastInputData> pssm_input( in BOOST_AUTO_TEST_CASE() local
673 CPssmEngine pssm_engine(pssm_input.get()); in BOOST_AUTO_TEST_CASE()
674 pssm_input->Process(); in BOOST_AUTO_TEST_CASE()
763 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
775 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
788 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
802 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
807 CPssmEngine pssm_engine(pssm_input.get()); in BOOST_AUTO_TEST_CASE()
868 auto_ptr<IPssmInputData> pssm_input in BOOST_AUTO_TEST_CASE() local
878 (_PSIPackedMsaNew(pssm_input->GetData())); in BOOST_AUTO_TEST_CASE()
[all …]
H A Dpssmenginefreqratios_unit_test.cpp87 auto_ptr<IPssmInputFreqRatios> pssm_input; in BOOST_AUTO_TEST_CASE() local
88 pssm_input.reset(new CPsiBlastInputFreqRatios in BOOST_AUTO_TEST_CASE()
90 CPssmEngine pssm_engine(pssm_input.get()); in BOOST_AUTO_TEST_CASE()
110 pssm_input->GetQuery()[i], j); in BOOST_AUTO_TEST_CASE()
133 CPsiBlastInputClustalW pssm_input(in, *opts, "BLOSUM62", diags); in BOOST_AUTO_TEST_CASE() local
134 CPssmEngine pssm_engine(&pssm_input); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Ddeltablast.cpp116 CRef<CCddInputData> pssm_input( in Run() local
129 pssm_engine.Reset(new CPssmEngine(pssm_input.GetNonNullPointer())); in Run()
H A Dpssm_engine.cpp153 s_Validate(IPssmInputCdd* pssm_input) in s_Validate() argument
155 _ASSERT(pssm_input); in s_Validate()
157 if ( !pssm_input->GetData() ) { in s_Validate()
163 if (PSIBlastOptionsValidate(pssm_input->GetOptions(), &errors) != 0) { in s_Validate()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Ddeltablast.cpp116 CRef<CCddInputData> pssm_input( in Run() local
129 pssm_engine.Reset(new CPssmEngine(pssm_input.GetNonNullPointer())); in Run()
H A Dpssm_engine.cpp153 s_Validate(IPssmInputCdd* pssm_input) in s_Validate() argument
155 _ASSERT(pssm_input); in s_Validate()
157 if ( !pssm_input->GetData() ) { in s_Validate()
163 if (PSIBlastOptionsValidate(pssm_input->GetOptions(), &errors) != 0) { in s_Validate()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/
H A Dblast_args.cpp1228 CPsiBlastInputClustalW pssm_input(input_stream, *psiblast_opts, in x_CreatePssmFromMsa() local
1233 CPssmEngine pssm_engine(&pssm_input); in x_CreatePssmFromMsa()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/
H A Dblast_args.cpp1228 CPsiBlastInputClustalW pssm_input(input_stream, *psiblast_opts, in x_CreatePssmFromMsa() local
1233 CPssmEngine pssm_engine(&pssm_input); in x_CreatePssmFromMsa()