blast_mt_unit_test.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiexpt.hpp>
#include <corelib/ncbiutil.hpp>
#include <corelib/ncbistre.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <algo/blast/api/objmgrfree_query_data.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/blastinput/blast_scope_src.hpp>
#include <algo/blast/api/local_db_adapter.hpp>
#include <algo/blast/format/blast_format.hpp>
#include <algo/blast/format/blast_async_format.hpp>
#include <algo/blast/format/build_archive.hpp>
#include <corelib/test_boost.hpp>
#include <common/test_assert.h>

Include dependency graph for blast_mt_unit_test.cpp:

Go to the source code of this file.

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Classes
class	CDLTestThread
class	CDLTest2Thread
class	CSeqDBTestThread
class	CSeqDBTest2Thread
class	CSeqDBTest3Thread

Macros
#define	NCBI_BOOST_NO_AUTO_TEST_MAIN

Functions
void	s_GenerateGiList (CRef< CSeqDB > &seqdb, vector< TGi > &gis)
void	s_GenerateAccsList (CRef< CSeqDB > &seqdb, vector< string > &ids)
void	s_MTDataLoaderTest (string &db, bool isProtein)
	BOOST_AUTO_TEST_CASE (MT_DataLoaderForEachThread_16S)
	BOOST_AUTO_TEST_CASE (MT_DataLoaderForEachThread_RefseqProt)
void	s_MTDataLoaderTest2 (string &db, bool isProtein)
	BOOST_AUTO_TEST_CASE (MT_SingleDataLoaderForAllThreads_16s)
	BOOST_AUTO_TEST_CASE (MT_SingleDataLoaderForAllThreads_ProtSelect)
void	s_MTSeqDBTest (string &db, bool isProtein)
	BOOST_AUTO_TEST_CASE (SeqDBTest_AccsToOid_nr)
	BOOST_AUTO_TEST_CASE (SeqDBTest_AccsToOid_nt)
void	s_MTSeqDBTest2 (string &db, bool isProtein)
	BOOST_AUTO_TEST_CASE (SeqDBTest2)
void	s_MTSeqDBTest3 (string &db, bool isProtein)
	BOOST_AUTO_TEST_CASE (SeqDBTest3)

Macro Definition Documentation

NCBI_BOOST_NO_AUTO_TEST_MAIN

#define NCBI_BOOST_NO_AUTO_TEST_MAIN

Definition at line 61 of file blast_mt_unit_test.cpp.

Function Documentation

BOOST_AUTO_TEST_CASE() [1/8]

BOOST_AUTO_TEST_CASE

(

MT_DataLoaderForEachThread_16S

)

Definition at line 165 of file blast_mt_unit_test.cpp.

References s_MTDataLoaderTest().

BOOST_AUTO_TEST_CASE() [2/8]

BOOST_AUTO_TEST_CASE

(

MT_DataLoaderForEachThread_RefseqProt

)

Definition at line 172 of file blast_mt_unit_test.cpp.

References s_MTDataLoaderTest().

BOOST_AUTO_TEST_CASE() [3/8]

BOOST_AUTO_TEST_CASE

(

MT_SingleDataLoaderForAllThreads_16s

)

Definition at line 230 of file blast_mt_unit_test.cpp.

References s_MTDataLoaderTest2().

BOOST_AUTO_TEST_CASE() [4/8]

BOOST_AUTO_TEST_CASE

(

MT_SingleDataLoaderForAllThreads_ProtSelect

)

Definition at line 239 of file blast_mt_unit_test.cpp.

References s_MTDataLoaderTest2().

BOOST_AUTO_TEST_CASE() [5/8]

BOOST_AUTO_TEST_CASE

(

SeqDBTest2

)

Definition at line 362 of file blast_mt_unit_test.cpp.

References s_MTSeqDBTest2().

BOOST_AUTO_TEST_CASE() [6/8]

BOOST_AUTO_TEST_CASE

(

SeqDBTest3

)

Definition at line 419 of file blast_mt_unit_test.cpp.

References s_MTSeqDBTest3().

BOOST_AUTO_TEST_CASE() [7/8]

BOOST_AUTO_TEST_CASE

(

SeqDBTest_AccsToOid_nr

)

Definition at line 294 of file blast_mt_unit_test.cpp.

References s_MTSeqDBTest().

BOOST_AUTO_TEST_CASE() [8/8]

BOOST_AUTO_TEST_CASE

(

SeqDBTest_AccsToOid_nt

)

Definition at line 303 of file blast_mt_unit_test.cpp.

References s_MTSeqDBTest().

s_GenerateAccsList()

void s_GenerateAccsList	(	CRef< CSeqDB > &	seqdb,
		vector< string > &	ids
	)

Definition at line 93 of file blast_mt_unit_test.cpp.

References CSeqDB::GetNumSeqs(), CSeqDB::GetSeqIDs(), CSeq_id::GetSeqIdString(), MIN, and t.

Referenced by s_MTSeqDBTest().

s_GenerateGiList()

void s_GenerateGiList	(	CRef< CSeqDB > &	seqdb,
		vector< TGi > &	gis
	)

Definition at line 75 of file blast_mt_unit_test.cpp.

References MIN.

Referenced by s_MTDataLoaderTest(), and s_MTDataLoaderTest2().

s_MTDataLoaderTest()

void s_MTDataLoaderTest	(	string &	db,
		bool	isProtein
	)

Definition at line 146 of file blast_mt_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::eProtein, i, and s_GenerateGiList().

Referenced by BOOST_AUTO_TEST_CASE().

s_MTDataLoaderTest2()

void s_MTDataLoaderTest2	(	string &	db,
		bool	isProtein
	)

Definition at line 205 of file blast_mt_unit_test.cpp.

References CObjectManager::eDefault, CSeqDB::eNucleotide, CSeqDB::eProtein, CObjectManager::GetInstance(), CBlastDbDataLoader::GetLoaderNameFromArgs(), i, CBlastDatabaseArgs::kSubjectsDataLoaderPriority, CBlastDbDataLoader::RegisterInObjectManager(), and s_GenerateGiList().

Referenced by BOOST_AUTO_TEST_CASE().

s_MTSeqDBTest()

void s_MTSeqDBTest	(	string &	db,
		bool	isProtein
	)

Definition at line 272 of file blast_mt_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::GetNumSeqs(), i, MIN, and s_GenerateAccsList().

Referenced by BOOST_AUTO_TEST_CASE().

s_MTSeqDBTest2()

void s_MTSeqDBTest2	(	string &	db,
		bool	isProtein
	)

Definition at line 336 of file blast_mt_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::GetNumSeqs(), i, and CSeqDB::SetNumberOfThreads().

Referenced by BOOST_AUTO_TEST_CASE().

s_MTSeqDBTest3()

void s_MTSeqDBTest3	(	string &	db,
		bool	isProtein
	)

Definition at line 392 of file blast_mt_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::GetNumSeqs(), i, and CSeqDB::SetNumberOfThreads().

Referenced by BOOST_AUTO_TEST_CASE().