Home
last modified time | relevance | path

Searched refs:db_adapter (Results 1 – 25 of 71) sorted by relevance

123

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/magicblast/
H A Dmagicblast_app.cpp103 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blast/
H A Dblastp_node.cpp101 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()
H A Dblastx_node.cpp102 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()
H A Dtblastn_node.cpp105 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()
H A Dpsiblast_app.cpp98 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 …]
H A Dblastn_node.cpp102 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()
H A Dtblastx_app.cpp116 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()
H A Drpsblast_node.cpp103 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()
H A Drpstblastn_node.cpp102 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()
H A Dseedtop_app.cpp158 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()
H A Dtblastn_app.cpp133 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()
H A Ddeltablast_app.cpp91 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 …]
H A Dblastp_app.cpp134 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blast/
H A Dblastp_node.cpp101 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()
H A Dblastx_node.cpp102 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()
H A Dtblastn_node.cpp105 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()
H A Dpsiblast_app.cpp98 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 …]
H A Dblastn_node.cpp102 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()
H A Dtblastx_app.cpp116 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()
H A Drpsblast_node.cpp103 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()
H A Drpstblastn_node.cpp102 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()
H A Dseedtop_app.cpp158 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()
H A Dtblastn_app.cpp133 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()
H A Ddeltablast_app.cpp91 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/rmblastn/
H A Drmblastn_app.cpp99 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()

123