blast_scope_src_unit_test.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <algo/blast/blastinput/blast_scope_src.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objects/entrez2/entrez2_client.hpp>
#include <objmgr/seq_vector.hpp>
#include <algo/blast/blastinput/blast_input.hpp>
#include <algo/blast/blastinput/blast_fasta_input.hpp>
#include <algo/blast/api/sseqloc.hpp>
#include "blast_input_unit_test_aux.hpp"

Include dependency graph for blast_scope_src_unit_test.cpp:

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Classes
struct	SDiagRestorer

Macros
#define	NCBI_TEST_APPLICATION
#define	NCBI_BOOST_NO_AUTO_TEST_MAIN

Functions
	USING_SCOPE (blast)
	USING_SCOPE (objects)
	BOOST_AUTO_TEST_CASE (RetrieveFromBlastDb_TestSequenceData)
	BOOST_AUTO_TEST_CASE (RetrieveFromDefaultBlastDb_NoNcbirc)
	BOOST_AUTO_TEST_CASE (RetrieveFromBlastDbOnly_TestSequenceDataWithAccession)
	BOOST_AUTO_TEST_CASE (ConfigFileTest_RetrieveFromBlastDb_TestSequenceData)
	BOOST_AUTO_TEST_CASE (ConfigFileTest_RetrieveFromNonStandardBlastDb_Config_TestSequenceData)
	BOOST_AUTO_TEST_CASE (ConfigFileTest_RetrieveFromNonStandardBlastDb_ForcedDb_TestSequenceData)
	BOOST_AUTO_TEST_CASE (ConfigFileTest_RetrieveFromGenbank_TestSequenceData)
	BOOST_AUTO_TEST_CASE (ConfigFileTest_UseNoDataLoaders)
static void	s_RetrieveSequenceLength (TGi gi, const string &dbname, bool is_prot, TSeqPos kExpectedLength)
	BOOST_AUTO_TEST_CASE (RetrieveFromBlastDb)
	BOOST_AUTO_TEST_CASE (RetrieveFromGenbank)
	BOOST_AUTO_TEST_CASE (RetrieveFromGenbank_NewlyAddedSequenceToGenbank)
	BOOST_AUTO_TEST_CASE (RetrieveFromGenbank_NoBlastDbDataLoader)
	BOOST_AUTO_TEST_CASE (RetrieveFromGenbank_IncorrectBlastDbType)
	BOOST_AUTO_TEST_CASE (InvalidBlastDatabase)
	BOOST_AUTO_TEST_CASE (ForceRemoteBlastDbLoader)
	BOOST_AUTO_TEST_CASE (RetrieveSeqUsingPDBIds)

Variables
	USING_NCBI_SCOPE

Macro Definition Documentation

NCBI_BOOST_NO_AUTO_TEST_MAIN

#define NCBI_BOOST_NO_AUTO_TEST_MAIN

Definition at line 34 of file blast_scope_src_unit_test.cpp.

NCBI_TEST_APPLICATION

#define NCBI_TEST_APPLICATION

Definition at line 32 of file blast_scope_src_unit_test.cpp.

Function Documentation

BOOST_AUTO_TEST_CASE() [1/16]

BOOST_AUTO_TEST_CASE

(

ConfigFileTest_RetrieveFromBlastDb_TestSequenceData

)

Definition at line 170 of file blast_scope_src_unit_test.cpp.

References CBioseq_Handle::eCoding_Iupac, SDataLoaderConfig::eUseBlastDbDataLoader, CScope::GetBioseqHandle(), CBlastScopeSourceWrapper::GetBlastDbLoaderName(), CBioseq_Handle::GetSeqVector(), i, SDataLoaderConfig::kDefaultProteinBlastDb, SDataLoaderConfig::m_BlastDbName, SDataLoaderConfig::m_UseBlastDbs, SDataLoaderConfig::m_UseGenbank, CBlastScopeSourceWrapper::NewScope(), CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), CSeqVector::size(), and string.

BOOST_AUTO_TEST_CASE() [2/16]

BOOST_AUTO_TEST_CASE

(

ConfigFileTest_RetrieveFromGenbank_TestSequenceData

)

Definition at line 262 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, CBioseq_Handle::eCoding_Iupac, SDataLoaderConfig::eUseGenbankDataLoader, CScope::GetBioseqHandle(), CBlastScopeSourceWrapper::GetBlastDbLoaderName(), CBioseq_Handle::GetSeqVector(), i, kEmptyStr, SDataLoaderConfig::m_BlastDbName, SDataLoaderConfig::m_UseBlastDbs, SDataLoaderConfig::m_UseGenbank, CBlastScopeSourceWrapper::NewScope(), and CSeqVector::size().

BOOST_AUTO_TEST_CASE() [3/16]

BOOST_AUTO_TEST_CASE

(

ConfigFileTest_RetrieveFromNonStandardBlastDb_Config_TestSequenceData

)

Definition at line 201 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, CBioseq_Handle::eCoding_Iupac, SDataLoaderConfig::eUseBlastDbDataLoader, CScope::GetBioseqHandle(), CBlastScopeSourceWrapper::GetBlastDbLoaderName(), CBioseq_Handle::GetSeqVector(), i, SDataLoaderConfig::m_BlastDbName, SDataLoaderConfig::m_UseBlastDbs, SDataLoaderConfig::m_UseGenbank, CBlastScopeSourceWrapper::NewScope(), CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), and CSeqVector::size().

BOOST_AUTO_TEST_CASE() [4/16]

BOOST_AUTO_TEST_CASE

(

ConfigFileTest_RetrieveFromNonStandardBlastDb_ForcedDb_TestSequenceData

)

Definition at line 232 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, CBioseq_Handle::eCoding_Iupac, SDataLoaderConfig::eUseBlastDbDataLoader, CScope::GetBioseqHandle(), CBlastScopeSourceWrapper::GetBlastDbLoaderName(), CBioseq_Handle::GetSeqVector(), i, SDataLoaderConfig::m_BlastDbName, SDataLoaderConfig::m_UseBlastDbs, SDataLoaderConfig::m_UseGenbank, CBlastScopeSourceWrapper::NewScope(), CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), and CSeqVector::size().

BOOST_AUTO_TEST_CASE() [5/16]

BOOST_AUTO_TEST_CASE

(

ConfigFileTest_UseNoDataLoaders

)

Definition at line 288 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, SDataLoaderConfig::eUseNoDataLoaders, CScope::GetBioseqHandle(), CBlastScopeSourceWrapper::GetBlastDbLoaderName(), kEmptyStr, SDataLoaderConfig::m_BlastDbName, SDataLoaderConfig::m_UseBlastDbs, SDataLoaderConfig::m_UseGenbank, CBlastScopeSourceWrapper::NewScope(), and CBioseq_Handle::State_NoData().

BOOST_AUTO_TEST_CASE() [6/16]

BOOST_AUTO_TEST_CASE

(

ForceRemoteBlastDbLoader

)

Definition at line 389 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, env, SDataLoaderConfig::eUseBlastDbDataLoader, CBlastScopeSourceWrapper::GetBlastDbLoaderName(), GetLength(), SDataLoaderConfig::kDefaultProteinBlastDb, kEmptyStr, SDataLoaderConfig::m_BlastDbName, SDataLoaderConfig::m_UseBlastDbs, SDataLoaderConfig::m_UseGenbank, CBlastScopeSourceWrapper::NewScope(), CAutoNcbiConfigFile::RemoveBLASTDBEnvVar(), CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), and string.

BOOST_AUTO_TEST_CASE() [7/16]

BOOST_AUTO_TEST_CASE

(

InvalidBlastDatabase

)

Definition at line 379 of file blast_scope_src_unit_test.cpp.

References CException::GetMsg(), NPOS, and s_RetrieveSequenceLength().

BOOST_AUTO_TEST_CASE() [8/16]

BOOST_AUTO_TEST_CASE

(

RetrieveFromBlastDb

)

Definition at line 327 of file blast_scope_src_unit_test.cpp.

References s_RetrieveSequenceLength().

BOOST_AUTO_TEST_CASE() [9/16]

BOOST_AUTO_TEST_CASE

(

RetrieveFromBlastDb_TestSequenceData

)

Definition at line 65 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, CBioseq_Handle::eCoding_Iupac, CScope::GetBioseqHandle(), CBlastScopeSourceWrapper::GetBlastDbLoaderName(), CBioseq_Handle::GetSeqVector(), i, SDataLoaderConfig::kDefaultProteinBlastDb, SDataLoaderConfig::m_BlastDbName, CBlastScopeSourceWrapper::NewScope(), CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), CSeqVector::size(), and string.

BOOST_AUTO_TEST_CASE() [10/16]

BOOST_AUTO_TEST_CASE

(

RetrieveFromBlastDbOnly_TestSequenceDataWithAccession

)

Definition at line 127 of file blast_scope_src_unit_test.cpp.

References CBioseq_Handle::eCoding_Iupac, SDataLoaderConfig::eUseBlastDbDataLoader, CScope::GetBioseqHandle(), CBlastScopeSourceWrapper::GetBlastDbLoaderName(), CBioseq_Handle::GetSeqVector(), i, ITERATE, SDataLoaderConfig::m_BlastDbName, msg(), CBlastScopeSourceWrapper::NewScope(), and CSeqVector::size().

BOOST_AUTO_TEST_CASE() [11/16]

BOOST_AUTO_TEST_CASE

(

RetrieveFromDefaultBlastDb_NoNcbirc

)

Definition at line 94 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, CBioseq_Handle::eCoding_Iupac, CMetaRegistry::fAlwaysReload, CScope::GetBioseqHandle(), CBlastScopeSourceWrapper::GetBlastDbLoaderName(), CBioseq_Handle::GetSeqVector(), i, CNcbiRegistry::IncludeNcbircIfAllowed(), CNcbiApplication::Instance(), SDataLoaderConfig::kDefaultProteinBlastDb, SDataLoaderConfig::m_BlastDbName, NcbiTestGetRWConfig(), CBlastScopeSourceWrapper::NewScope(), CNcbiApplicationAPI::ReloadConfig(), CSeqVector::size(), and string.

BOOST_AUTO_TEST_CASE() [12/16]

BOOST_AUTO_TEST_CASE

(

RetrieveFromGenbank

)

Definition at line 332 of file blast_scope_src_unit_test.cpp.

References s_RetrieveSequenceLength().

BOOST_AUTO_TEST_CASE() [13/16]

BOOST_AUTO_TEST_CASE

(

RetrieveFromGenbank_IncorrectBlastDbType

)

Definition at line 368 of file blast_scope_src_unit_test.cpp.

References s_RetrieveSequenceLength().

BOOST_AUTO_TEST_CASE() [14/16]

BOOST_AUTO_TEST_CASE

(

RetrieveFromGenbank_NewlyAddedSequenceToGenbank

)

Definition at line 336 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, GetLength(), CBlastScopeSourceWrapper::NewScope(), CEntrez2Client::Query(), results, s_RetrieveSequenceLength(), and t.

BOOST_AUTO_TEST_CASE() [15/16]

BOOST_AUTO_TEST_CASE

(

RetrieveFromGenbank_NoBlastDbDataLoader

)

Definition at line 359 of file blast_scope_src_unit_test.cpp.

References CSeq_id_Base::e_Gi, GetLength(), and CBlastScopeSourceWrapper::NewScope().

BOOST_AUTO_TEST_CASE() [16/16]

BOOST_AUTO_TEST_CASE

(

RetrieveSeqUsingPDBIds

)

Definition at line 416 of file blast_scope_src_unit_test.cpp.

References dbname(), GetLength(), SDataLoaderConfig::m_BlastDbName, SDataLoaderConfig::m_UseGenbank, CBlastScopeSourceWrapper::NewScope(), CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), NStr::Split(), and NStr::StringToInt().

s_RetrieveSequenceLength()

static void s_RetrieveSequenceLength ( TGi  gi, const string &  dbname, bool  is_prot, TSeqPos  kExpectedLength  )

static

Definition at line 306 of file blast_scope_src_unit_test.cpp.

References dbname(), CSeq_id_Base::e_Gi, GetLength(), SDataLoaderConfig::m_BlastDbName, SDataLoaderConfig::m_UseBlastDbs, SDataLoaderConfig::m_UseGenbank, CBlastScopeSourceWrapper::NewScope(), CAutoNcbiConfigFile::SetNucleotideBlastDbDataLoader(), and CAutoNcbiConfigFile::SetProteinBlastDbDataLoader().

Referenced by BOOST_AUTO_TEST_CASE().

USING_SCOPE() [1/2]

USING_SCOPE

(

blast

)

USING_SCOPE() [2/2]

USING_SCOPE

(

objects

)

Variable Documentation

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 52 of file blast_scope_src_unit_test.cpp.