blast_services_test.cpp File Reference

#include <ncbi_pch.hpp>
#include <objtools/blast/services/blast_services.hpp>
#include <corelib/ncbienv.hpp>
#include <serial/serial.hpp>
#include <serial/objostr.hpp>
#include <serial/exception.hpp>
#include <util/range.hpp>
#include <objects/blast/Blast4_database.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <corelib/test_boost.hpp>

Include dependency graph for blast_services_test.cpp:

Go to the source code of this file.

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Macros
#define	NCBI_TEST_APPLICATION

Functions
static bool	s_HasRawSequence (const CBioseq &bioseq)
	NCBITEST_AUTO_INIT ()
	NCBITEST_AUTO_FINI ()
	BOOST_AUTO_TEST_CASE (GetInformationAboutInvalidBlastDatabaseRemotely)
	BOOST_AUTO_TEST_CASE (MultipleDatabaseValidityCheck)
	BOOST_AUTO_TEST_CASE (EmptyStringValidityCheck)
	BOOST_AUTO_TEST_CASE (OneBadDbValidityCheck)
	BOOST_AUTO_TEST_CASE (GetWindowMaskedTaxIds)
	BOOST_AUTO_TEST_CASE (GetDatabaseInfo)
	BOOST_AUTO_TEST_CASE (GetBioseq)
	BOOST_AUTO_TEST_CASE (FetchQuerySequence_NonExistentDb)
	BOOST_AUTO_TEST_CASE (FetchQuerySequence_NoQueries)
	BOOST_AUTO_TEST_CASE (FetchMultipleSequences)
	BOOST_AUTO_TEST_CASE (FetchMultipleSequences_NotFound)
	BOOST_AUTO_TEST_CASE (FetchQuerySequenceInfo_NonExistentDb)
	BOOST_AUTO_TEST_CASE (FetchQuerySequenceInfo_NoQueries)
	BOOST_AUTO_TEST_CASE (FetchQuerySequenceInfo)
	BOOST_AUTO_TEST_CASE (FetchQuerySequenceInfo_NotFound)
	BOOST_AUTO_TEST_CASE (FetchMultipleSequencesInfo)
	BOOST_AUTO_TEST_CASE (FetchMultipleSequencesInfo_NotFound)
	BOOST_AUTO_TEST_CASE (FetchQuerySequenceParts_NonExistentDb)
	BOOST_AUTO_TEST_CASE (FetchQuerySequenceParts_NoQueries)
	BOOST_AUTO_TEST_CASE (FetchQuerySequenceParts)
	BOOST_AUTO_TEST_CASE (FetchQuerySequenceParts_NotFound)
	BOOST_AUTO_TEST_CASE (FetchMultipleSequencesParts)
	BOOST_AUTO_TEST_CASE (FetchMultipleSequencesParts_NotFound)

Variables
	USING_NCBI_SCOPE

Macro Definition Documentation

NCBI_TEST_APPLICATION

#define NCBI_TEST_APPLICATION

Definition at line 34 of file blast_services_test.cpp.

Function Documentation

BOOST_AUTO_TEST_CASE() [1/23]

BOOST_AUTO_TEST_CASE

(

EmptyStringValidityCheck

)

Definition at line 122 of file blast_services_test.cpp.

References CBlastServices::IsValidBlastDb().

BOOST_AUTO_TEST_CASE() [2/23]

BOOST_AUTO_TEST_CASE

(

FetchMultipleSequences

)

Definition at line 326 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequences(), i, ITERATE, kSeqType, results, and s_HasRawSequence().

BOOST_AUTO_TEST_CASE() [3/23]

BOOST_AUTO_TEST_CASE

(

FetchMultipleSequences_NotFound

)

Definition at line 364 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequences(), i, NStr::IntToString(), kSeqType, NPOS, and results.

BOOST_AUTO_TEST_CASE() [4/23]

BOOST_AUTO_TEST_CASE

(

FetchMultipleSequencesInfo

)

Definition at line 471 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequencesInfo(), i, ITERATE, kSeqType, results, and s_HasRawSequence().

BOOST_AUTO_TEST_CASE() [5/23]

BOOST_AUTO_TEST_CASE

(

FetchMultipleSequencesInfo_NotFound

)

Definition at line 509 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequencesInfo(), i, NStr::IntToString(), kSeqType, NPOS, and results.

BOOST_AUTO_TEST_CASE() [6/23]

BOOST_AUTO_TEST_CASE

(

FetchMultipleSequencesParts

)

Definition at line 625 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequenceParts(), i, ITERATE, kSeqType, compile_time_bits::range(), results, and val.

BOOST_AUTO_TEST_CASE() [7/23]

BOOST_AUTO_TEST_CASE

(

FetchMultipleSequencesParts_NotFound

)

Definition at line 669 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequenceParts(), i, NStr::IntToString(), kSeqType, NPOS, compile_time_bits::range(), results, and val.

BOOST_AUTO_TEST_CASE() [8/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequence_NonExistentDb

)

Definition at line 296 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequences(), and results.

BOOST_AUTO_TEST_CASE() [9/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequence_NoQueries

)

Definition at line 313 of file blast_services_test.cpp.

References CBlastServices::GetSequences(), and results.

BOOST_AUTO_TEST_CASE() [10/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequenceInfo

)

Definition at line 423 of file blast_services_test.cpp.

References CBlastServices::GetSequencesInfo(), results, and s_HasRawSequence().

BOOST_AUTO_TEST_CASE() [11/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequenceInfo_NonExistentDb

)

Definition at line 392 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequencesInfo(), and results.

BOOST_AUTO_TEST_CASE() [12/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequenceInfo_NoQueries

)

Definition at line 409 of file blast_services_test.cpp.

References CBlastServices::GetSequencesInfo(), and results.

BOOST_AUTO_TEST_CASE() [13/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequenceInfo_NotFound

)

Definition at line 446 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequencesInfo(), NStr::IntToString(), NPOS, and results.

BOOST_AUTO_TEST_CASE() [14/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequenceParts

)

Definition at line 574 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequenceParts(), compile_time_bits::range(), and results.

BOOST_AUTO_TEST_CASE() [15/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequenceParts_NonExistentDb

)

Definition at line 537 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequenceParts(), and results.

BOOST_AUTO_TEST_CASE() [16/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequenceParts_NoQueries

)

Definition at line 557 of file blast_services_test.cpp.

References CBlastServices::GetSequenceParts(), and results.

BOOST_AUTO_TEST_CASE() [17/23]

BOOST_AUTO_TEST_CASE

(

FetchQuerySequenceParts_NotFound

)

Definition at line 599 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, CBlastServices::GetSequenceParts(), NStr::IntToString(), NPOS, compile_time_bits::range(), and results.

BOOST_AUTO_TEST_CASE() [18/23]

BOOST_AUTO_TEST_CASE

(

GetBioseq

)

Definition at line 284 of file blast_services_test.cpp.

References CSeq_id_Base::e_Gi, GetLength(), CBlastServices::GetSequences(), and results.

BOOST_AUTO_TEST_CASE() [19/23]

BOOST_AUTO_TEST_CASE

(

GetDatabaseInfo

)

Definition at line 205 of file blast_services_test.cpp.

References eBlast4_residue_type_nucleotide, eBlast4_residue_type_protein, eBlast4_residue_type_unknown, CRef< C, Locker >::Empty(), CBlastServices::GetDatabaseInfo(), CRef< C, Locker >::NotEmpty(), CBlast4_database_Base::SetName(), CBlast4_database_Base::SetType(), and NStr::StartsWith().

BOOST_AUTO_TEST_CASE() [20/23]

BOOST_AUTO_TEST_CASE

(

GetInformationAboutInvalidBlastDatabaseRemotely

)

Definition at line 108 of file blast_services_test.cpp.

References CBlastServices::IsValidBlastDb().

BOOST_AUTO_TEST_CASE() [21/23]

BOOST_AUTO_TEST_CASE

(

GetWindowMaskedTaxIds

)

Definition at line 193 of file blast_services_test.cpp.

References CBlastServices::GetTaxIdWithWindowMaskerSupport().

BOOST_AUTO_TEST_CASE() [22/23]

BOOST_AUTO_TEST_CASE

(

MultipleDatabaseValidityCheck

)

Definition at line 115 of file blast_services_test.cpp.

References CBlastServices::IsValidBlastDb().

BOOST_AUTO_TEST_CASE() [23/23]

BOOST_AUTO_TEST_CASE

(

OneBadDbValidityCheck

)

Definition at line 129 of file blast_services_test.cpp.

References CBlastServices::IsValidBlastDb().

NCBITEST_AUTO_FINI()

NCBITEST_AUTO_FINI

(

)

Definition at line 102 of file blast_services_test.cpp.

NCBITEST_AUTO_INIT()

NCBITEST_AUTO_INIT

(

)

Definition at line 96 of file blast_services_test.cpp.

s_HasRawSequence()

static bool s_HasRawSequence ( const CBioseq &  bioseq )

static

Definition at line 72 of file blast_services_test.cpp.

References CSeq_inst_Base::CanGetSeq_data(), CDelta_seq_Base::e_Loc, CSeq_inst_Base::eRepr_delta, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::IsSetExt(), and ITERATE.

Referenced by BOOST_AUTO_TEST_CASE().

Variable Documentation

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 68 of file blast_services_test.cpp.