#include <ncbi_pch.hpp>#include <corelib/ncbiapp.hpp>#include <algo/blast/api/magicblast.hpp>#include <algo/blast/api/magicblast_options.hpp>#include <algo/blast/api/blast_usage_report.hpp>#include <algo/blast/blastinput/blast_fasta_input.hpp>#include <algo/blast/blastinput/blast_asn1_input.hpp>#include <algo/blast/blast_sra_input/blast_sra_input.hpp>#include <algo/blast/blastinput/magicblast_args.hpp>#include <algo/blast/api/objmgr_query_data.hpp>#include <algo/blast/format/blast_format.hpp>#include <objtools/align_format/align_format_util.hpp>#include "../blast/blast_app_util.hpp"#include <algo/blast/api/objmgrfree_query_data.hpp>#include <objects/seqset/Seq_entry.hpp>#include "magicblast_util.hpp"#include "magicblast_thread.hpp"
Include dependency graph for magicblast_app.cpp:
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Classes | |
| class | CMagicBlastVersion |
| class | CMagicBlastApp |
Functions | |
| USING_SCOPE (blast) | |
| USING_SCOPE (objects) | |
| static CShortReadFastaInputSource::EInputFormat | s_QueryOptsInFmtToFastaInFmt (CMapperQueryOptionsArgs::EInputFormat infmt) |
| static CBlastInputSourceOMF * | s_CreateInputSource (CRef< CMapperQueryOptionsArgs > query_opts, CRef< CMagicBlastAppArgs > cmd_line_args) |
| static void | s_InitializeSubject (CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, CRef< blast::CLocalDbAdapter > &db_adapter, Uint8 &subject_length, int &num_sequences) |
| static bool | s_IsIStreamEmpty (CNcbiIstream &in) |
| static string | s_GetCmdlineArgs (const CNcbiArguments &a) |
| int | NcbiSys_main (int argc, ncbi::TXChar *argv[]) |
Variables | |
| USING_NCBI_SCOPE | |
| static const int | kMajorVersion = 1 |
| static const int | kMinorVersion = 7 |
| static const int | kPatchVersion = 2 |
Function Documentation
◆ NcbiSys_main()
| int NcbiSys_main | ( | int | argc, |
| ncbi::TXChar * | argv[] | ||
| ) |
Definition at line 542 of file magicblast_app.cpp.
References CNcbiApplicationAPI::AppMain().
◆ s_CreateInputSource()
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static |
Definition at line 154 of file magicblast_app.cpp.
References CMapperQueryOptionsArgs::eASN1bin, CMapperQueryOptionsArgs::eASN1text, CMapperQueryOptionsArgs::eFasta, CMapperQueryOptionsArgs::eFastc, CMapperQueryOptionsArgs::eFastq, CSraException::eNotFoundDb, CMapperQueryOptionsArgs::eSra, CSraException::GetErrCode(), CMapperQueryOptionsArgs::GetInputFormat(), CBlastAppArgs::GetInputStream(), CMapperQueryOptionsArgs::GetMateInputStream(), CMapperQueryOptionsArgs::GetSraAccessions(), CMapperQueryOptionsArgs::HasMateInputStream(), CMapperQueryOptionsArgs::IsPaired(), CMapperQueryOptionsArgs::IsSraCacheEnabled(), NCBI_THROW, s_QueryOptsInFmtToFastaInFmt(), and str().
Referenced by CMagicBlastApp::Run().
◆ s_GetCmdlineArgs()
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static |
Definition at line 288 of file magicblast_app.cpp.
References a, cmd, i, and kEmptyStr.
Referenced by CMagicBlastApp::Run().
◆ s_InitializeSubject()
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static |
Definition at line 226 of file magicblast_app.cpp.
References _ASSERT, BlastSeqSrcGetNumSeqs(), BlastSeqSrcGetTotLen(), CRef< C, Locker >::Empty(), CObjectManager::GetInstance(), CSeqDB::GetNumSeqs(), CSearchDatabase::GetSeqDb(), CSeqDB::GetTotalLength(), CRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().
Referenced by CMagicBlastApp::Run().
◆ s_IsIStreamEmpty()
|
static |
Definition at line 264 of file magicblast_app.cpp.
References in().
Referenced by CMagicBlastApp::Run().
◆ s_QueryOptsInFmtToFastaInFmt()
|
static |
Definition at line 128 of file magicblast_app.cpp.
References CMapperQueryOptionsArgs::eFasta, CShortReadFastaInputSource::eFasta, CMapperQueryOptionsArgs::eFastc, CShortReadFastaInputSource::eFastc, CMapperQueryOptionsArgs::eFastq, CShortReadFastaInputSource::eFastq, and NCBI_THROW.
Referenced by s_CreateInputSource().
◆ USING_SCOPE() [1/2]
| USING_SCOPE | ( | blast | ) |
◆ USING_SCOPE() [2/2]
| USING_SCOPE | ( | objects | ) |
Variable Documentation
◆ kMajorVersion
Definition at line 60 of file magicblast_app.cpp.
◆ kMinorVersion
Definition at line 61 of file magicblast_app.cpp.
◆ kPatchVersion
Definition at line 62 of file magicblast_app.cpp.
◆ USING_NCBI_SCOPE
| USING_NCBI_SCOPE |
Definition at line 55 of file magicblast_app.cpp.
