| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
| H A D | optionshandle_unit_test.cpp | 96 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
106 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
116 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
126 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
136 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
146 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
156 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
166 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
176 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
186 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
[all …]
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
| H A D | optionshandle_unit_test.cpp | 96 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
106 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
116 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
126 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
136 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
146 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
156 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
166 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
176 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
186 (*m_OptsHandle, in BOOST_FIXTURE_TEST_CASE()
[all …]
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
| H A D | bl2seq.cpp | 57 m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); in BEGIN_SCOPE()
64 _ASSERT( !m_OptsHandle.Empty() ); in x_InitCLocalBlast()
67 CRef<CLocalDbAdapter> db(new CLocalDbAdapter(subject_factory, m_OptsHandle, m_DbScanMode)); in x_InitCLocalBlast()
68 m_Blast.Reset(new CLocalBlast(query_factory, m_OptsHandle, db)); in x_InitCLocalBlast()
74 m_OptsHandle->SetHitlistSize((int) m_tSubjects.size()); in x_InitCLocalBlast()
87 m_OptsHandle.Reset(&opts); in CBl2Seq()
98 m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); in CBl2Seq()
109 m_OptsHandle.Reset(&opts); in CBl2Seq()
117 m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); in CBl2Seq()
125 m_OptsHandle.Reset(&opts); in CBl2Seq()
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| H A D | local_db_adapter.cpp | 64 m_OptsHandle(opts_handle), m_DbName(kEmptyStr), m_DbScanMode(dbscan_mode) in CLocalDbAdapter()
130 } else if (m_SubjectFactory.NotEmpty() && m_OptsHandle.NotEmpty()) { in MakeSeqSrc()
132 m_OptsHandle->GetOptions().GetProgramType(); in MakeSeqSrc()
158 } else if (m_SubjectFactory.NotEmpty() && m_OptsHandle.NotEmpty()) { in MakeSeqInfoSrc()
159 EBlastProgramType p(m_OptsHandle->GetOptions().GetProgramType()); in MakeSeqInfoSrc()
183 } else if (m_OptsHandle) { in IsProtein()
184 const EBlastProgramType p = m_OptsHandle->GetOptions().GetProgramType(); in IsProtein()
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| H A D | psiblast_impl.cpp | 62 : m_Pssm(pssm), m_Query(0), m_Subject(subject), m_OptsHandle(options), in BEGIN_SCOPE()
73 : m_Pssm(0), m_Query(query), m_Subject(subject), m_OptsHandle(options), in CPsiBlastImpl()
83 if (m_OptsHandle.Empty()) { in x_Validate()
86 m_OptsHandle->Validate(); in x_Validate()
92 CPsiBlastValidate::QueryFactory(m_Query, *m_OptsHandle); in x_Validate()
110 PsiBlastComputePssmScores(m_Pssm, m_OptsHandle->GetOptions()); in x_CreatePssmScoresFromFrequencyRatios()
125 opts(const_cast<CBlastOptions*>(&m_OptsHandle->GetOptions())); in Run()
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| H A D | psiblast_impl.hpp | 112 CConstRef<CBlastOptionsHandle> m_OptsHandle; member in CPsiBlastImpl
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
| H A D | bl2seq.cpp | 57 m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); in BEGIN_SCOPE()
64 _ASSERT( !m_OptsHandle.Empty() ); in x_InitCLocalBlast()
67 CRef<CLocalDbAdapter> db(new CLocalDbAdapter(subject_factory, m_OptsHandle, m_DbScanMode)); in x_InitCLocalBlast()
68 m_Blast.Reset(new CLocalBlast(query_factory, m_OptsHandle, db)); in x_InitCLocalBlast()
74 m_OptsHandle->SetHitlistSize((int) m_tSubjects.size()); in x_InitCLocalBlast()
87 m_OptsHandle.Reset(&opts); in CBl2Seq()
98 m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); in CBl2Seq()
109 m_OptsHandle.Reset(&opts); in CBl2Seq()
117 m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); in CBl2Seq()
125 m_OptsHandle.Reset(&opts); in CBl2Seq()
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| H A D | local_db_adapter.cpp | 64 m_OptsHandle(opts_handle), m_DbName(kEmptyStr), m_DbScanMode(dbscan_mode) in CLocalDbAdapter()
130 } else if (m_SubjectFactory.NotEmpty() && m_OptsHandle.NotEmpty()) { in MakeSeqSrc()
132 m_OptsHandle->GetOptions().GetProgramType(); in MakeSeqSrc()
158 } else if (m_SubjectFactory.NotEmpty() && m_OptsHandle.NotEmpty()) { in MakeSeqInfoSrc()
159 EBlastProgramType p(m_OptsHandle->GetOptions().GetProgramType()); in MakeSeqInfoSrc()
183 } else if (m_OptsHandle) { in IsProtein()
184 const EBlastProgramType p = m_OptsHandle->GetOptions().GetProgramType(); in IsProtein()
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| H A D | psiblast_impl.cpp | 62 : m_Pssm(pssm), m_Query(0), m_Subject(subject), m_OptsHandle(options), in BEGIN_SCOPE()
73 : m_Pssm(0), m_Query(query), m_Subject(subject), m_OptsHandle(options), in CPsiBlastImpl()
83 if (m_OptsHandle.Empty()) { in x_Validate()
86 m_OptsHandle->Validate(); in x_Validate()
92 CPsiBlastValidate::QueryFactory(m_Query, *m_OptsHandle); in x_Validate()
110 PsiBlastComputePssmScores(m_Pssm, m_OptsHandle->GetOptions()); in x_CreatePssmScoresFromFrequencyRatios()
125 opts(const_cast<CBlastOptions*>(&m_OptsHandle->GetOptions())); in Run()
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| H A D | psiblast_impl.hpp | 112 CConstRef<CBlastOptionsHandle> m_OptsHandle; member in CPsiBlastImpl
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/proteinkmer/ |
| H A D | kblastapi.hpp | 63 m_OptsHandle(optsHndl), in CBlastKmerSearch()
69 : m_OptsHandle(optsHndl), in CBlastKmerSearch()
93 CRef<CBlastpKmerOptionsHandle> m_OptsHandle; member in CBlastKmerSearch
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/proteinkmer/ |
| H A D | kblastapi.hpp | 63 m_OptsHandle(optsHndl), in CBlastKmerSearch()
69 : m_OptsHandle(optsHndl), in CBlastKmerSearch()
93 CRef<CBlastpKmerOptionsHandle> m_OptsHandle; member in CBlastKmerSearch
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/proteinkmer/ |
| H A D | kblastapi.cpp | 159 if (m_OptsHandle->GetDbLength() == 0) in Run()
160 m_OptsHandle->SetDbLength(seqdb->GetTotalLength()); in Run()
162 CBlastpKmerOptionsHandle* kmerOptHndl = dynamic_cast<CBlastpKmerOptionsHandle*> (&*m_OptsHandle); in Run()
215 …CLocalBlast lcl_blast(qfactory, CRef<CBlastOptionsHandle> (m_OptsHandle.GetPointer()), seq_src, se… in Run()
231 …CRef<CSearchResultSet> my_blast_results=s_MakeEmptyResults(qfactory, m_OptsHandle->GetOptions(), C… in Run()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/proteinkmer/ |
| H A D | kblastapi.cpp | 159 if (m_OptsHandle->GetDbLength() == 0) in Run()
160 m_OptsHandle->SetDbLength(seqdb->GetTotalLength()); in Run()
162 CBlastpKmerOptionsHandle* kmerOptHndl = dynamic_cast<CBlastpKmerOptionsHandle*> (&*m_OptsHandle); in Run()
215 …CLocalBlast lcl_blast(qfactory, CRef<CBlastOptionsHandle> (m_OptsHandle.GetPointer()), seq_src, se… in Run()
231 …CRef<CSearchResultSet> my_blast_results=s_MakeEmptyResults(qfactory, m_OptsHandle->GetOptions(), C… in Run()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/ |
| H A D | bl2seq.hpp | 183 CRef<CBlastOptionsHandle> m_OptsHandle; ///< Blast options member in CBl2Seq
281 return *m_OptsHandle; in SetOptionsHandle()
287 return *m_OptsHandle; in GetOptionsHandle()
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| H A D | local_db_adapter.hpp | 144 CConstRef<CBlastOptionsHandle> m_OptsHandle; member in CLocalDbAdapter
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/api/ |
| H A D | bl2seq.hpp | 183 CRef<CBlastOptionsHandle> m_OptsHandle; ///< Blast options member in CBl2Seq
281 return *m_OptsHandle; in SetOptionsHandle()
287 return *m_OptsHandle; in GetOptionsHandle()
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| H A D | local_db_adapter.hpp | 144 CConstRef<CBlastOptionsHandle> m_OptsHandle; member in CLocalDbAdapter
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/ |
| H A D | blast_args.cpp | 3457 if (m_OptsHandle.NotEmpty()) { in SetOptions()
3458 CBlastOptions& opts = m_OptsHandle->SetOptions(); in SetOptions()
3474 try { m_OptsHandle->Validate(); } in SetOptions()
3479 return m_OptsHandle; in SetOptions()
3595 EBlastProgramType prog = m_OptsHandle->GetOptions().GetProgramType(); in x_IssueWarningsForIgnoredOptions()
3668 if(m_OptsHandle.Empty()) in SetOptionsForSavedStrategy()
3676 CBlastOptions& opts = m_OptsHandle->SetOptions(); in SetOptionsForSavedStrategy()
3697 try { m_OptsHandle->Validate(); } in SetOptionsForSavedStrategy()
3701 return m_OptsHandle; in SetOptionsForSavedStrategy()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/ |
| H A D | blast_args.cpp | 3457 if (m_OptsHandle.NotEmpty()) { in SetOptions()
3458 CBlastOptions& opts = m_OptsHandle->SetOptions(); in SetOptions()
3474 try { m_OptsHandle->Validate(); } in SetOptions()
3479 return m_OptsHandle; in SetOptions()
3595 EBlastProgramType prog = m_OptsHandle->GetOptions().GetProgramType(); in x_IssueWarningsForIgnoredOptions()
3668 if(m_OptsHandle.Empty()) in SetOptionsForSavedStrategy()
3676 CBlastOptions& opts = m_OptsHandle->SetOptions(); in SetOptionsForSavedStrategy()
3697 try { m_OptsHandle->Validate(); } in SetOptionsForSavedStrategy()
3701 return m_OptsHandle; in SetOptionsForSavedStrategy()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/blastinput/ |
| H A D | blast_args.hpp | 1422 m_OptsHandle = opts_hndl; in SetOptionsHandle()
1520 CRef<CBlastOptionsHandle> m_OptsHandle; member in CBlastAppArgs
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/blastinput/ |
| H A D | blast_args.hpp | 1422 m_OptsHandle = opts_hndl; in SetOptionsHandle()
1520 CRef<CBlastOptionsHandle> m_OptsHandle; member in CBlastAppArgs
|