/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/magicblast/ |
H A D | magicblast_app.cpp | 103 CRef<CLocalDbAdapter> db_adapter, 228 CRef<blast::CLocalDbAdapter>& db_adapter, in s_InitializeSubject() argument 232 db_adapter.Reset(); in s_InitializeSubject() 250 BlastSeqSrc* seq_src = db_adapter->MakeSeqSrc(); in s_InitializeSubject() 258 db_adapter.Reset(new CLocalDbAdapter(*search_db)); in s_InitializeSubject() 322 CRef<CLocalDbAdapter> db_adapter; in Run() local 325 s_InitializeSubject(db_args, opts_hndl, db_adapter, db_size, in Run() 327 _ASSERT(db_adapter); in Run() 458 x_LogBlastSearchInfo(m_UsageReport, opt, fmt_args, db_adapter, in Run() 480 if (db_adapter->IsBlastDb()) { in x_LogBlastSearchInfo() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blast/ |
H A D | blastp_node.cpp | 101 CRef<CLocalDbAdapter> db_adapter; in Main() local 103 InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), db_adapter, scope); in Main() 104 _ASSERT(db_adapter && scope); in Main() 107 CheckMTByQueries_DBSize(db_adapter, opt); in Main() 115 db_adapter); in Main() 130 CBlastFormat formatter(opt, *db_adapter, in Main() 144 db_adapter->GetFilteringAlgorithm(), in Main() 177 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Main()
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H A D | blastx_node.cpp | 102 CRef<CLocalDbAdapter> db_adapter; in Main() local 104 InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), db_adapter, scope); in Main() 105 _ASSERT(db_adapter && scope); in Main() 108 CheckMTByQueries_DBSize(db_adapter, opt); in Main() 116 db_adapter); in Main() 134 CBlastFormat formatter(opt, *db_adapter, in Main() 148 db_adapter->GetFilteringAlgorithm(), in Main() 181 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Main()
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H A D | tblastn_node.cpp | 105 CRef<CLocalDbAdapter> db_adapter; in Main() local 107 InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), db_adapter, scope); in Main() 108 _ASSERT(db_adapter && scope); in Main() 111 CheckMTByQueries_DBSize(db_adapter, opt); in Main() 121 db_adapter); in Main() 158 CBlastFormat formatter(opt, *db_adapter, in Main() 172 db_adapter->GetFilteringAlgorithm(), in Main() 205 CLocalBlast lcl_blast(query_factory, opts_hndl, db_adapter); in Main() 240 CRef<CPsiBlast> psiblast(new CPsiBlast(pssm, db_adapter, psi_opts)); in Main()
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H A D | psiblast_app.cpp | 98 CRef<CLocalDbAdapter> db_adapter, 105 CRef<CLocalDbAdapter> db_adapter, 331 CRef<CLocalDbAdapter> db_adapter, in DoIterations() argument 442 CRef<CLocalDbAdapter> db_adapter; in Run() local 445 db_adapter, scope); in Run() 446 _ASSERT(db_adapter && scope); in Run() 456 db_adapter); in Run() 482 CBlastFormat formatter(opt, *db_adapter, in Run() 496 db_adapter->GetFilteringAlgorithm(), in Run() 521 db_adapter, in Run() [all …]
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H A D | blastn_node.cpp | 102 CRef<CLocalDbAdapter> db_adapter; in Main() local 104 InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), db_adapter, scope); in Main() 105 _ASSERT(db_adapter && scope); in Main() 108 CheckMTByQueries_DBSize(db_adapter, opt); in Main() 116 db_adapter); in Main() 140 CBlastFormat formatter(opt, *db_adapter, in Main() 154 db_adapter->GetFilteringAlgorithm(), in Main() 201 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Main()
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H A D | tblastx_app.cpp | 116 CRef<CLocalDbAdapter> db_adapter; in Run() local 119 db_adapter, scope); in Run() 120 _ASSERT(db_adapter && scope); in Run() 127 db_adapter); in Run() 145 CBlastFormat formatter(opt, *db_adapter, in Run() 159 db_adapter->GetFilteringAlgorithm(), in Run() 192 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Run()
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H A D | rpsblast_node.cpp | 103 CRef<CLocalDbAdapter> db_adapter; in Main() local 106 db_adapter, scope); in Main() 107 _ASSERT(db_adapter && scope); in Main() 114 db_adapter); in Main() 128 CBlastFormat formatter(opt, *db_adapter, in Main() 142 db_adapter->GetFilteringAlgorithm(), in Main()
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H A D | rpstblastn_node.cpp | 102 CRef<CLocalDbAdapter> db_adapter; in Main() local 105 db_adapter, scope); in Main() 106 _ASSERT(db_adapter && scope); in Main() 113 db_adapter); in Main() 127 CBlastFormat formatter(opt, *db_adapter, in Main() 141 db_adapter->GetFilteringAlgorithm(), in Main()
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H A D | seedtop_app.cpp | 158 CRef<CLocalDbAdapter> db_adapter; in Run() local 172 db_adapter.Reset(new CLocalDbAdapter(qf, opts_hndl)); in Run() 179 db_adapter.Reset(new CLocalDbAdapter(*db)); in Run() 186 _ASSERT(db_adapter); in Run() 194 CSeedTop::TSeedTopResults results = seed_top.Run(db_adapter); in Run() 229 db_adapter->ResetBlastSeqSrcIteration(); in Run()
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H A D | tblastn_app.cpp | 133 CRef<CLocalDbAdapter> db_adapter; in x_RunMTBySplitDB() local 136 db_adapter, scope); in x_RunMTBySplitDB() 137 _ASSERT(db_adapter && scope); in x_RunMTBySplitDB() 146 db_adapter); in x_RunMTBySplitDB() 185 CBlastFormat formatter(opt, *db_adapter, in x_RunMTBySplitDB() 199 db_adapter->GetFilteringAlgorithm(), in x_RunMTBySplitDB() 232 CLocalBlast lcl_blast(query_factory, opts_hndl, db_adapter); in x_RunMTBySplitDB() 267 CRef<CPsiBlast> psiblast(new CPsiBlast(pssm, db_adapter, psi_opts)); in x_RunMTBySplitDB()
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H A D | deltablast_app.cpp | 91 CRef<CLocalDbAdapter> db_adapter, 215 CRef<CLocalDbAdapter> db_adapter; in Run() local 218 db_adapter, scope); in Run() 219 _ASSERT(db_adapter && scope); in Run() 226 db_adapter); in Run() 263 CBlastFormat formatter(opt, *db_adapter, in Run() 277 db_adapter->GetFilteringAlgorithm(), in Run() 322 deltablast.Reset(new CDeltaBlast(queries, db_adapter, in Run() 429 db_adapter, in Run() 472 CRef<CLocalDbAdapter> db_adapter, in DoPsiBlastIterations() argument [all …]
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H A D | blastp_app.cpp | 134 CRef<CLocalDbAdapter> db_adapter; in x_RunMTBySplitDB() local 137 db_adapter, scope); in x_RunMTBySplitDB() 138 _ASSERT(db_adapter && scope); in x_RunMTBySplitDB() 145 db_adapter); in x_RunMTBySplitDB() 164 CBlastFormat formatter(opt, *db_adapter, in x_RunMTBySplitDB() 178 db_adapter->GetFilteringAlgorithm(), in x_RunMTBySplitDB() 211 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in x_RunMTBySplitDB()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blast/ |
H A D | blastp_node.cpp | 101 CRef<CLocalDbAdapter> db_adapter; in Main() local 103 InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), db_adapter, scope); in Main() 104 _ASSERT(db_adapter && scope); in Main() 107 CheckMTByQueries_DBSize(db_adapter, opt); in Main() 115 db_adapter); in Main() 130 CBlastFormat formatter(opt, *db_adapter, in Main() 144 db_adapter->GetFilteringAlgorithm(), in Main() 177 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Main()
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H A D | blastx_node.cpp | 102 CRef<CLocalDbAdapter> db_adapter; in Main() local 104 InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), db_adapter, scope); in Main() 105 _ASSERT(db_adapter && scope); in Main() 108 CheckMTByQueries_DBSize(db_adapter, opt); in Main() 116 db_adapter); in Main() 134 CBlastFormat formatter(opt, *db_adapter, in Main() 148 db_adapter->GetFilteringAlgorithm(), in Main() 181 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Main()
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H A D | tblastn_node.cpp | 105 CRef<CLocalDbAdapter> db_adapter; in Main() local 107 InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), db_adapter, scope); in Main() 108 _ASSERT(db_adapter && scope); in Main() 111 CheckMTByQueries_DBSize(db_adapter, opt); in Main() 121 db_adapter); in Main() 158 CBlastFormat formatter(opt, *db_adapter, in Main() 172 db_adapter->GetFilteringAlgorithm(), in Main() 205 CLocalBlast lcl_blast(query_factory, opts_hndl, db_adapter); in Main() 240 CRef<CPsiBlast> psiblast(new CPsiBlast(pssm, db_adapter, psi_opts)); in Main()
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H A D | psiblast_app.cpp | 98 CRef<CLocalDbAdapter> db_adapter, 105 CRef<CLocalDbAdapter> db_adapter, 331 CRef<CLocalDbAdapter> db_adapter, in DoIterations() argument 442 CRef<CLocalDbAdapter> db_adapter; in Run() local 445 db_adapter, scope); in Run() 446 _ASSERT(db_adapter && scope); in Run() 456 db_adapter); in Run() 482 CBlastFormat formatter(opt, *db_adapter, in Run() 496 db_adapter->GetFilteringAlgorithm(), in Run() 521 db_adapter, in Run() [all …]
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H A D | blastn_node.cpp | 102 CRef<CLocalDbAdapter> db_adapter; in Main() local 104 InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), db_adapter, scope); in Main() 105 _ASSERT(db_adapter && scope); in Main() 108 CheckMTByQueries_DBSize(db_adapter, opt); in Main() 116 db_adapter); in Main() 140 CBlastFormat formatter(opt, *db_adapter, in Main() 154 db_adapter->GetFilteringAlgorithm(), in Main() 201 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Main()
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H A D | tblastx_app.cpp | 116 CRef<CLocalDbAdapter> db_adapter; in Run() local 119 db_adapter, scope); in Run() 120 _ASSERT(db_adapter && scope); in Run() 127 db_adapter); in Run() 145 CBlastFormat formatter(opt, *db_adapter, in Run() 159 db_adapter->GetFilteringAlgorithm(), in Run() 192 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Run()
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H A D | rpsblast_node.cpp | 103 CRef<CLocalDbAdapter> db_adapter; in Main() local 106 db_adapter, scope); in Main() 107 _ASSERT(db_adapter && scope); in Main() 114 db_adapter); in Main() 128 CBlastFormat formatter(opt, *db_adapter, in Main() 142 db_adapter->GetFilteringAlgorithm(), in Main()
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H A D | rpstblastn_node.cpp | 102 CRef<CLocalDbAdapter> db_adapter; in Main() local 105 db_adapter, scope); in Main() 106 _ASSERT(db_adapter && scope); in Main() 113 db_adapter); in Main() 127 CBlastFormat formatter(opt, *db_adapter, in Main() 141 db_adapter->GetFilteringAlgorithm(), in Main()
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H A D | seedtop_app.cpp | 158 CRef<CLocalDbAdapter> db_adapter; in Run() local 172 db_adapter.Reset(new CLocalDbAdapter(qf, opts_hndl)); in Run() 179 db_adapter.Reset(new CLocalDbAdapter(*db)); in Run() 186 _ASSERT(db_adapter); in Run() 194 CSeedTop::TSeedTopResults results = seed_top.Run(db_adapter); in Run() 229 db_adapter->ResetBlastSeqSrcIteration(); in Run()
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H A D | tblastn_app.cpp | 133 CRef<CLocalDbAdapter> db_adapter; in x_RunMTBySplitDB() local 136 db_adapter, scope); in x_RunMTBySplitDB() 137 _ASSERT(db_adapter && scope); in x_RunMTBySplitDB() 146 db_adapter); in x_RunMTBySplitDB() 185 CBlastFormat formatter(opt, *db_adapter, in x_RunMTBySplitDB() 199 db_adapter->GetFilteringAlgorithm(), in x_RunMTBySplitDB() 232 CLocalBlast lcl_blast(query_factory, opts_hndl, db_adapter); in x_RunMTBySplitDB() 267 CRef<CPsiBlast> psiblast(new CPsiBlast(pssm, db_adapter, psi_opts)); in x_RunMTBySplitDB()
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H A D | deltablast_app.cpp | 91 CRef<CLocalDbAdapter> db_adapter, 215 CRef<CLocalDbAdapter> db_adapter; in Run() local 218 db_adapter, scope); in Run() 219 _ASSERT(db_adapter && scope); in Run() 226 db_adapter); in Run() 263 CBlastFormat formatter(opt, *db_adapter, in Run() 277 db_adapter->GetFilteringAlgorithm(), in Run() 322 deltablast.Reset(new CDeltaBlast(queries, db_adapter, in Run() 429 db_adapter, in Run() 472 CRef<CLocalDbAdapter> db_adapter, in DoPsiBlastIterations() argument [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/rmblastn/ |
H A D | rmblastn_app.cpp | 99 CRef<CLocalDbAdapter> db_adapter; in Run() local 102 db_adapter, scope); in Run() 103 _ASSERT(db_adapter && scope); in Run() 114 CBlastFormat formatter(opt, *db_adapter, in Run() 128 db_adapter->GetFilteringAlgorithm(), in Run() 152 CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); in Run()
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