| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blast/ |
| H A D | blast_app_util.cpp | 85 CRef<blast::CBlastDatabaseArgs> db_args, in InitializeRemoteBlast()
163 InitializeSubject(CRef<blast::CBlastDatabaseArgs> db_args, in InitializeSubject()
250 (int)CBlastDatabaseArgs::kSubjectsDataLoaderPriority in RegisterOMDataLoader()
258 CRef<blast::CBlastDatabaseArgs> db_args, in s_InitializeExportStrategy()
315 CRef<blast::CBlastDatabaseArgs> db_args, in s_ExportSearchStrategy()
436 static CRef<blast::CBlastDatabaseArgs>
443 CRef<CBlastDatabaseArgs> db_args(new CBlastDatabaseArgs); in s_ImportDatabase()
511 static CRef<blast::CBlastDatabaseArgs>
515 CRef<CBlastDatabaseArgs> db_args(new CBlastDatabaseArgs); in s_ImportSubjects()
563 CRef<blast::CBlastDatabaseArgs> db_args; in s_ImportSearchStrategy()
[all …]
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| H A D | blast_formatter.cpp | 258 s_InitializeSubject(CRef<blast::CBlastDatabaseArgs> db_args, in s_InitializeSubject()
291 …scope->AddDataLoader(RegisterOMDataLoader(seqdb), CBlastDatabaseArgs::kSubjectsDataLoaderPriority); in s_InitializeSubject()
302 … true, CObjectManager::eDefault, CBlastDatabaseArgs::kSubjectsDataLoaderPriority) in s_InitializeSubject()
304 scope->AddDataLoader(remote_loader, CBlastDatabaseArgs::kSubjectsDataLoaderPriority); in s_InitializeSubject()
362 CRef<CBlastDatabaseArgs> db_args(new CBlastDatabaseArgs()); // FIXME, what about rpsblast? in PrintFormattedOutput()
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| H A D | deltablast_app.cpp | 89 CRef<CBlastDatabaseArgs> db_args,
214 CRef<CBlastDatabaseArgs> db_args(m_CmdLineArgs->GetBlastDatabaseArgs()); in Run()
256 CBlastDatabaseArgs::kSubjectsDataLoaderPriority - 1); in Run()
470 CRef<CBlastDatabaseArgs> db_args, in DoPsiBlastIterations()
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| H A D | blast_app_util.hpp | 112 CRef<blast::CBlastDatabaseArgs> db_args,
126 InitializeSubject(CRef<blast::CBlastDatabaseArgs> db_args,
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| H A D | psiblast_app.cpp | 97 CRef<CBlastDatabaseArgs> db_args,
330 CRef<CBlastDatabaseArgs> db_args, in DoIterations()
441 CRef<CBlastDatabaseArgs> db_args(m_CmdLineArgs->GetBlastDatabaseArgs()); in Run()
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| H A D | blast_report.cpp | 282 CRef<CBlastDatabaseArgs> db_args(new CBlastDatabaseArgs()); // FIXME, what about rpsblast? in PrintFormattedOutput()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blast/ |
| H A D | blast_app_util.cpp | 85 CRef<blast::CBlastDatabaseArgs> db_args, in InitializeRemoteBlast()
179 InitializeSubject(CRef<blast::CBlastDatabaseArgs> db_args, in InitializeSubject()
266 (int)CBlastDatabaseArgs::kSubjectsDataLoaderPriority in RegisterOMDataLoader()
274 CRef<blast::CBlastDatabaseArgs> db_args, in s_InitializeExportStrategy()
331 CRef<blast::CBlastDatabaseArgs> db_args, in s_ExportSearchStrategy()
452 static CRef<blast::CBlastDatabaseArgs>
459 CRef<CBlastDatabaseArgs> db_args(new CBlastDatabaseArgs); in s_ImportDatabase()
527 static CRef<blast::CBlastDatabaseArgs>
531 CRef<CBlastDatabaseArgs> db_args(new CBlastDatabaseArgs); in s_ImportSubjects()
579 CRef<blast::CBlastDatabaseArgs> db_args; in s_ImportSearchStrategy()
[all …]
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| H A D | blast_formatter.cpp | 258 s_InitializeSubject(CRef<blast::CBlastDatabaseArgs> db_args, in s_InitializeSubject()
291 …scope->AddDataLoader(RegisterOMDataLoader(seqdb), CBlastDatabaseArgs::kSubjectsDataLoaderPriority); in s_InitializeSubject()
302 … true, CObjectManager::eDefault, CBlastDatabaseArgs::kSubjectsDataLoaderPriority) in s_InitializeSubject()
304 scope->AddDataLoader(remote_loader, CBlastDatabaseArgs::kSubjectsDataLoaderPriority); in s_InitializeSubject()
362 CRef<CBlastDatabaseArgs> db_args(new CBlastDatabaseArgs()); // FIXME, what about rpsblast? in PrintFormattedOutput()
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| H A D | deltablast_app.cpp | 89 CRef<CBlastDatabaseArgs> db_args,
214 CRef<CBlastDatabaseArgs> db_args(m_CmdLineArgs->GetBlastDatabaseArgs()); in Run()
256 CBlastDatabaseArgs::kSubjectsDataLoaderPriority - 1); in Run()
470 CRef<CBlastDatabaseArgs> db_args, in DoPsiBlastIterations()
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| H A D | blast_app_util.hpp | 112 CRef<blast::CBlastDatabaseArgs> db_args,
126 InitializeSubject(CRef<blast::CBlastDatabaseArgs> db_args,
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| H A D | psiblast_app.cpp | 97 CRef<CBlastDatabaseArgs> db_args,
330 CRef<CBlastDatabaseArgs> db_args, in DoIterations()
441 CRef<CBlastDatabaseArgs> db_args(m_CmdLineArgs->GetBlastDatabaseArgs()); in Run()
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| H A D | blast_report.cpp | 282 CRef<CBlastDatabaseArgs> db_args(new CBlastDatabaseArgs()); // FIXME, what about rpsblast? in PrintFormattedOutput()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/magicblast/ |
| H A D | magicblast_thread.hpp | 53 CRef<CBlastDatabaseArgs> db_args,
66 CRef<CBlastDatabaseArgs> m_DatabaseArgs;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/proteinkmer/demo/ |
| H A D | kblastthr.hpp | 67 CRef<CBlastDatabaseArgs> db_args, in CBlastKmerThread()
92 CRef<CBlastDatabaseArgs> m_DbArgs;
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| H A D | kblastp_app.cpp | 119 CRef<CBlastDatabaseArgs> db_args(m_CmdLineArgs->GetBlastDatabaseArgs()); in Run()
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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 | 882 class NCBI_BLASTINPUT_EXPORT CBlastDatabaseArgs : public IBlastCmdLineArgs class
903 CBlastDatabaseArgs(bool request_mol_type = false,
1004 CBlastDatabaseArgs::kSubjectsDataLoaderPriority); in AddIgSequenceScope()
1426 CRef<CBlastDatabaseArgs> GetBlastDatabaseArgs() const { in GetBlastDatabaseArgs()
1430 void SetBlastDatabaseArgs(CRef<CBlastDatabaseArgs> args) { in SetBlastDatabaseArgs()
1503 CRef<CBlastDatabaseArgs> m_BlastDbArgs;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/blastinput/ |
| H A D | blast_args.hpp | 882 class NCBI_BLASTINPUT_EXPORT CBlastDatabaseArgs : public IBlastCmdLineArgs class
903 CBlastDatabaseArgs(bool request_mol_type = false,
1004 CBlastDatabaseArgs::kSubjectsDataLoaderPriority); in AddIgSequenceScope()
1426 CRef<CBlastDatabaseArgs> GetBlastDatabaseArgs() const { in GetBlastDatabaseArgs()
1430 void SetBlastDatabaseArgs(CRef<CBlastDatabaseArgs> args) { in SetBlastDatabaseArgs()
1503 CRef<CBlastDatabaseArgs> m_BlastDbArgs;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/ |
| H A D | kblastp_args.cpp | 54 m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, false, false, false, true)); in CKBlastpAppArgs()
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| H A D | tblastx_args.cpp | 57 m_BlastDbArgs.Reset(new CBlastDatabaseArgs); in CTblastxAppArgs()
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| H A D | igblastn_args.cpp | 73 m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, false, true)); in CIgBlastnAppArgs()
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| H A D | igblastp_args.cpp | 75 m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, false, true)); in CIgBlastpAppArgs()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/ |
| H A D | kblastp_args.cpp | 54 m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, false, false, false, true)); in CKBlastpAppArgs()
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| H A D | tblastx_args.cpp | 57 m_BlastDbArgs.Reset(new CBlastDatabaseArgs); in CTblastxAppArgs()
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| H A D | igblastn_args.cpp | 73 m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, false, true)); in CIgBlastnAppArgs()
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| H A D | rmblastn_args.cpp | 46 m_BlastDbArgs.Reset(new CBlastDatabaseArgs); in CRMBlastnAppArgs()
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