#include <ncbi_pch.hpp>
#include <objtools/blast/seqdb_reader/seqdbexpert.hpp>
#include <objtools/blast/seqdb_reader/column_reader.hpp>
#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>
#include <objects/blastdb/defline_extra.hpp>
#include <serial/serialbase.hpp>
#include <objects/seq/seq__.hpp>
#include <corelib/ncbifile.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/blast/seqdb_reader/impl/seqdbisam.hpp>
#include <cmath>
#include <algorithm>
#include <random>
#include <chrono>
#include <corelib/test_boost.hpp>

Include dependency graph for seqdb_unit_test.cpp:

Go to the SVN repository for this file.

Classes
class	CTmpEnvironmentSetter

class	CSimpleGiList

class	CSeqIdList

class	CNegativeIdList

struct	SDbSumInfo

class	CTestThread

Macros
#define	NCBI_TEST_APPLICATION

#define	DEV_NULL "nul:"

#define	BEGIN(X) (X)

#define	END(X) ((X) + (sizeof (X) / sizeof *(X)))

Enumerations
enum	EMaskingType { eAll , eOdd , eEven , ePrime , eEND }

Functions
	USING_SCOPE (objects)

template<class A , class B , class C , class D , class E >
string	s_ToString (const A &a, const B &b, const C &c, const D &d, const E &e)

static void	s_TestPartialAmbigRange (CSeqDB &db, int oid, int begin, int end)

static void	s_TestPartialAmbig (CSeqDB &db, TGi nt_gi)

static bool	s_MaskingTest (EMaskingType mask, unsigned oid)

static void	s_TestMaskingLimits (EMaskingType mask, unsigned first, unsigned last, unsigned lowest, unsigned highest, unsigned count)

template<class NUM , class DIF >
void	s_ApproxEqual (NUM a, NUM b, DIF epsilon, int lineno)

static Uint4	s_BufHash (const char *buf_in, Uint4 length, Uint4 start=1)

template<class ASNOBJ >
string	s_Stringify (CRef< ASNOBJ > a)

	BOOST_AUTO_TEST_CASE (ConstructLocal)

	BOOST_AUTO_TEST_CASE (PathDelimiters)

	BOOST_AUTO_TEST_CASE (ConstructMissing)

	BOOST_AUTO_TEST_CASE (InvalidSeqType)

	BOOST_AUTO_TEST_CASE (ValidPath)

	BOOST_AUTO_TEST_CASE (InvalidPath)

	BOOST_AUTO_TEST_CASE (SummaryDataN)

	BOOST_AUTO_TEST_CASE (SummaryDataP)

	BOOST_AUTO_TEST_CASE (GetAmbigSeqAllocN)

	BOOST_AUTO_TEST_CASE (GetAmbigSeqAllocP)

	BOOST_AUTO_TEST_CASE (GetAmbigSeqN)

	BOOST_AUTO_TEST_CASE (GetAmbigSeqP)

	BOOST_AUTO_TEST_CASE (GetBioseqN)

	BOOST_AUTO_TEST_CASE (GetBioseqP)

	BOOST_AUTO_TEST_CASE (GetHdrN)

	BOOST_AUTO_TEST_CASE (GetHdrP)

	BOOST_AUTO_TEST_CASE (GetSeqIDsN)

	BOOST_AUTO_TEST_CASE (GetSeqIDsP)

	BOOST_AUTO_TEST_CASE (GetSeqLength)

	BOOST_AUTO_TEST_CASE (GetSeqLengthApprox)

	BOOST_AUTO_TEST_CASE (GetSequenceN)

	BOOST_AUTO_TEST_CASE (GetSequenceP)

	BOOST_AUTO_TEST_CASE (NrAndSwissProt)

	BOOST_AUTO_TEST_CASE (TranslateIdents)

	BOOST_AUTO_TEST_CASE (StringIdentSearch)

	BOOST_AUTO_TEST_CASE (AmbigBioseq)

	BOOST_AUTO_TEST_CASE (GetLenHighOID)

	BOOST_AUTO_TEST_CASE (GetLenNegOID)

	BOOST_AUTO_TEST_CASE (GetSeqHighOID)

	BOOST_AUTO_TEST_CASE (GetSeqNegOID)

	BOOST_AUTO_TEST_CASE (Offset2OidBadOffset)

	BOOST_AUTO_TEST_CASE (Offset2OidBadOid)

	BOOST_AUTO_TEST_CASE (Offset2OidMonotony)

	BOOST_AUTO_TEST_CASE (OpenWithBLASTDBEnv)

	BOOST_AUTO_TEST_CASE (OpenWithoutBLASTDBEnv)

	BOOST_AUTO_TEST_CASE (GiLists)

	BOOST_AUTO_TEST_CASE (OidRanges)

	BOOST_AUTO_TEST_CASE (GiListOidRange)

	BOOST_AUTO_TEST_CASE (EmptyDBList)

	BOOST_AUTO_TEST_CASE (IsBinaryGiList_True)

	BOOST_AUTO_TEST_CASE (IsBinaryGiList_False)

	BOOST_AUTO_TEST_CASE (IsBinaryGiList_EmptyFile)

	BOOST_AUTO_TEST_CASE (IsBinaryGiList_InvalidFile)

	BOOST_AUTO_TEST_CASE (BinaryUserGiList)

	BOOST_AUTO_TEST_CASE (TextUserGiList)

	BOOST_AUTO_TEST_CASE (UserSeqIdList)

	BOOST_AUTO_TEST_CASE (CSeqDBFileGiList_GetGis)

	BOOST_AUTO_TEST_CASE (TwoGiListsOneVolume)

	BOOST_AUTO_TEST_CASE (GetTaxIDs_gi_to_taxid)

	BOOST_AUTO_TEST_CASE (GetLeafTaxIDs_gi_to_taxid_set)

	BOOST_AUTO_TEST_CASE (GetTaxIDs_vector_of_taxids)

	BOOST_AUTO_TEST_CASE (GetLeafTaxIDs_vector_of_taxids)

	BOOST_AUTO_TEST_CASE (PartialSequences)

	BOOST_AUTO_TEST_CASE (GiListInOidRangeIteration)

	BOOST_AUTO_TEST_CASE (SeqidToOid)

	BOOST_AUTO_TEST_CASE (TestResetInternalChunkBookmark)

	BOOST_AUTO_TEST_CASE (ExpertNullConstructor)

	BOOST_AUTO_TEST_CASE (ExpertTaxInfo)

	BOOST_AUTO_TEST_CASE (ExpertRawData)

	BOOST_AUTO_TEST_CASE (ExpertRawDataProteinNulls)

	BOOST_AUTO_TEST_CASE (ExpertRawDataLength)

	BOOST_AUTO_TEST_CASE (ExpertIdBounds)

	BOOST_AUTO_TEST_CASE (ExpertIdBoundsNoPig)

	BOOST_AUTO_TEST_CASE (ResolveDbPath)

	BOOST_AUTO_TEST_CASE (IntersectionGiList)

	BOOST_AUTO_TEST_CASE (IntersectionNegGiList)

	BOOST_AUTO_TEST_CASE (ComputedList)

	BOOST_AUTO_TEST_CASE (ComplexComputedList)

static bool	s_DbHasOID (CSeqDB &db, int &count, int oid)

	BOOST_AUTO_TEST_CASE (ComputedListFilter)

	BOOST_AUTO_TEST_CASE (SharedMemoryMaps)

	BOOST_AUTO_TEST_CASE (SeqIdList)

	BOOST_AUTO_TEST_CASE (OidToGiLookup)

	BOOST_AUTO_TEST_CASE (SeqIdListAndGiList)

	BOOST_AUTO_TEST_CASE (EmptyVolume)

	BOOST_AUTO_TEST_CASE (GetSeqData_Protein)

	BOOST_AUTO_TEST_CASE (GetSeqData_Nucleotide)

	BOOST_AUTO_TEST_CASE (OidRewriting)

	BOOST_AUTO_TEST_CASE (GetSequenceAsString)

	BOOST_AUTO_TEST_CASE (TotalLengths)

static void	s_ModifyMap (map< int, int > &m, int key, int c, int &total)

static void	s_MapAllGis (CSeqDB &db, map< int, int > &m, int change, int &total)

	BOOST_AUTO_TEST_CASE (NegativeGiList)

	BOOST_AUTO_TEST_CASE (NegativeListNt)

	BOOST_AUTO_TEST_CASE (NegativeListSwissprot)

	BOOST_AUTO_TEST_CASE (HashToOid)

	BOOST_AUTO_TEST_CASE (FilteredHeaders)

static void	s_CheckIdLookup (CSeqDB &db, const string &acc, size_t exp_oids, size_t exp_size)

	BOOST_AUTO_TEST_CASE (ProtOldTest)

	BOOST_AUTO_TEST_CASE (ProtTest)

	BOOST_AUTO_TEST_CASE (NuclOldTest)

	BOOST_AUTO_TEST_CASE (NuclTest)

	BOOST_AUTO_TEST_CASE (PdbIdWithChain)

	BOOST_AUTO_TEST_CASE (UserDefinedColumns)

	BOOST_AUTO_TEST_CASE (VersionedSparseId)

	BOOST_AUTO_TEST_CASE (MaskDataColumn)

	BOOST_AUTO_TEST_CASE (CheckColumnFailureCleanup)

	BOOST_AUTO_TEST_CASE (EmptyMaskData)

	BOOST_AUTO_TEST_CASE (OidAndGiLists)

	BOOST_AUTO_TEST_CASE (DeltaSequenceHash)

	BOOST_AUTO_TEST_CASE (RestartWithVolumes)

	BOOST_AUTO_TEST_CASE (ExtractBlastDefline)

	BOOST_AUTO_TEST_CASE (TestDiskUsage)

	BOOST_AUTO_TEST_CASE (FindGnomonIds)

	BOOST_AUTO_TEST_CASE (TestOidNotFoundWithUserAliasFileAndGiList)

	BOOST_AUTO_TEST_CASE (TestSpaceInDbName)

	BOOST_AUTO_TEST_CASE (MultiTaxidBlastDefLine)

	BOOST_AUTO_TEST_CASE (SingleTaxidBlastDefLine)

	BOOST_AUTO_TEST_CASE (CSeqDBIsam_32bit_GI)

	BOOST_AUTO_TEST_CASE (Test_SeqIdList_AliasFile)

	BOOST_AUTO_TEST_CASE (Test_SeqIdList_FilteredID)

	BOOST_AUTO_TEST_CASE (Test_Multi_SeqIdList_AliasFile)

	BOOST_AUTO_TEST_CASE (Test_Mix_GI_SeqId_List_AliasFile)

	BOOST_AUTO_TEST_CASE (Test_Mix_User_SeqIdList_AliasFile)

	BOOST_AUTO_TEST_CASE (PigListSwissprot)

	BOOST_AUTO_TEST_CASE (CombinedFilters)

	BOOST_AUTO_TEST_CASE (TaxFilterWithGiListDB)

	BOOST_AUTO_TEST_CASE (TestMemoryMapFile)

	BOOST_AUTO_TEST_CASE (TestMemoryMapFile_MT)

	BOOST_AUTO_TEST_CASE (TestTaxIdsLookup)

	BOOST_AUTO_TEST_CASE (TestTaxIdsLookup_v4)

Variables
	USING_NCBI_SCOPE

Macro Definition Documentation

◆ BEGIN

#define BEGIN ( X ) (X)

Definition at line 1774 of file seqdb_unit_test.cpp.

◆ DEV_NULL

#define DEV_NULL "nul:"

Definition at line 55 of file seqdb_unit_test.cpp.

◆ END

#define END ( X ) ((X) + (sizeof (X) / sizeof *(X)))

Definition at line 1775 of file seqdb_unit_test.cpp.

◆ NCBI_TEST_APPLICATION

#define NCBI_TEST_APPLICATION

Definition at line 32 of file seqdb_unit_test.cpp.

Enumeration Type Documentation

◆ EMaskingType

enum EMaskingType

Enumerator
eAll
eOdd
eEven
ePrime
eEND

Definition at line 73 of file seqdb_unit_test.cpp.

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/117]

BOOST_AUTO_TEST_CASE ( AmbigBioseq )

◆ BOOST_AUTO_TEST_CASE() [2/117]

BOOST_AUTO_TEST_CASE ( BinaryUserGiList )

Definition at line 1609 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), and CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [3/117]

BOOST_AUTO_TEST_CASE ( CheckColumnFailureCleanup )

Definition at line 3841 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, and CSeqDB::GetAvailableMaskAlgorithms().

◆ BOOST_AUTO_TEST_CASE() [4/117]

BOOST_AUTO_TEST_CASE ( CombinedFilters )

Definition at line 4340 of file seqdb_unit_test.cpp.

References CSeqDBGiList::AddPig(), CSeqDBGiList::AddTaxIds(), CSeqDBNegativeList::AddTaxIds(), CSeqDB::CheckOrFindOID(), CSeqDB::eProtein, CSeqDB::GetNumSeqs(), i, CSeqDBNegativeList::SetPigList(), t, and TAX_ID_CONST.

◆ BOOST_AUTO_TEST_CASE() [5/117]

BOOST_AUTO_TEST_CASE ( ComplexComputedList )

Definition at line 2504 of file seqdb_unit_test.cpp.

References CSeqDBIdSet::Compute(), CSeqDBIdSet::eAnd, CSeqDBIdSet::eGi, CSeqDBIdSet::eOr, CSeqDBIdSet::eXor, CSeqDBNegativeList::FindGi(), CSeqDBGiList::FindGi(), CSeqDBIdSet::GetNegativeList(), CSeqDBIdSet::GetPositiveList(), i, and CSeqDBIdSet::IsPositive().

◆ BOOST_AUTO_TEST_CASE() [6/117]

BOOST_AUTO_TEST_CASE ( ComputedList )

Definition at line 2456 of file seqdb_unit_test.cpp.

References CSeqDBIdSet::eAnd, CSeqDBIdSet::eGi, CSeqDBGiList::FindGi(), and i.

◆ BOOST_AUTO_TEST_CASE() [7/117]

BOOST_AUTO_TEST_CASE ( ComputedListFilter )

Definition at line 2626 of file seqdb_unit_test.cpp.

References all, CSeqDBIdSet::Blank(), CSeqDB::CheckOrFindOID(), CSeqDBIdSet::Compute(), CSeqDBIdSet::eAnd, CSeqDBIdSet::eGi, CSeqDB::eNucleotide, CSeqDBIdSet::eOr, CSeqDB::GetIdSet(), CSeqDB::GetNumOIDs(), and s_DbHasOID().

◆ BOOST_AUTO_TEST_CASE() [8/117]

BOOST_AUTO_TEST_CASE ( ConstructLocal )

Definition at line 257 of file seqdb_unit_test.cpp.

References CSeqDB::eFilteredAll, CSeqDB::eProtein, and CSeqDB::GetTotals().

◆ BOOST_AUTO_TEST_CASE() [9/117]

BOOST_AUTO_TEST_CASE ( ConstructMissing )

Definition at line 287 of file seqdb_unit_test.cpp.

References CSeqDB::eFilteredAll, CSeqDB::eProtein, and CSeqDB::GetTotals().

◆ BOOST_AUTO_TEST_CASE() [10/117]

BOOST_AUTO_TEST_CASE ( CSeqDBFileGiList_GetGis )

Definition at line 1657 of file seqdb_unit_test.cpp.

References CDirEntry::ConvertToOSPath(), CSeqDBGiList::GetGiList(), CSeqDBGiList::GetNumGis(), GI_FROM, i, kFileName, msg(), NStr::SizetToString(), and ct::sort().

◆ BOOST_AUTO_TEST_CASE() [11/117]

BOOST_AUTO_TEST_CASE ( CSeqDBIsam_32bit_GI )

Definition at line 4173 of file seqdb_unit_test.cpp.

References CSeq_id_Base::e_Gi, eGiId, CSeq_id_Base::GetGi(), GI_FROM, GI_TO, i, and CSeqDBIsam::IdToOid().

◆ BOOST_AUTO_TEST_CASE() [12/117]

BOOST_AUTO_TEST_CASE ( DeltaSequenceHash )

Definition at line 3982 of file seqdb_unit_test.cpp.

References CSeq_inst_Base::CanGetSeq_data(), CSeqDB::eNucleotide, f, CBioseq_Base::GetInst(), CDirEntry::GetPathSeparator(), CSeqDBExpert::GetSequenceHash(), CSeqDB::GiToOid(), MSerial_AsnText, SeqDB_SequenceHash(), and string.

◆ BOOST_AUTO_TEST_CASE() [13/117]

BOOST_AUTO_TEST_CASE ( EmptyDBList )

Definition at line 1568 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [14/117]

BOOST_AUTO_TEST_CASE ( EmptyMaskData )

Definition at line 3850 of file seqdb_unit_test.cpp.

References CSeqDB::TSequenceRanges::empty(), CSeqDB::eNucleotide, CSeqDB::GetAvailableMaskAlgorithms(), and CSeqDB::GetMaskData().

◆ BOOST_AUTO_TEST_CASE() [15/117]

BOOST_AUTO_TEST_CASE ( EmptyVolume )

Definition at line 2965 of file seqdb_unit_test.cpp.

References CSeqDB::AccessionToOids(), CSeqDB::Begin(), buffer, CSeqDB::CheckOrFindOID(), eAtlas, CRef< C, Locker >::Empty(), CSeqDB::eOidList, CSeqDB::eProtein, CSeqDB::eUnfilteredAll, CSeqDB::FindVolumePaths(), CSeqDB::GetAliasFileValues(), CSeqDB::GetAmbigSeq(), CSeqDB::GetAmbigSeqAlloc(), CSeqDB::GetBioseq(), CSeqDB::GetBioseqNoData(), CSeqDB::GetDate(), CSeqDB::GetDBNameList(), CSeqDB::GetGiList(), CSeqDB::GetGis(), CSeqDB::GetHdr(), CSeqDB::GetMaxLength(), CSeqDB::GetNextOIDChunk(), CSeqDB::GetNumOIDs(), CSeqDB::GetNumSeqs(), CSeqDB::GetOidAtOffset(), CSeqDB::GetSeqData(), CSeqDB::GetSeqIDs(), CSeqDB::GetSeqLength(), CSeqDB::GetSeqLengthApprox(), CSeqDB::GetSequence(), CSeqDB::GetSequenceType(), CSeqDB::GetTaxIDs(), CSeqDB::GetTaxInfo(), CSeqDB::GetTitle(), CSeqDB::GetTotalLength(), CSeqDB::GetTotals(), CSeqDB::GetVolumeLength(), CSeqDB::GiToBioseq(), CSeqDB::GiToOid(), CSeqDB::GiToPig(), info, kSeqDBNuclBlastNA8, NULL, CSeqDB::OidToGi(), CSeqDB::OidToPig(), CSeqDB::PigToBioseq(), CSeqDB::PigToGi(), CSeqDB::PigToOid(), CSeqDB::ResetInternalChunkBookmark(), CSeqDB::SeqidToBioseq(), CSeqDB::SeqidToOid(), CSeqDB::SeqidToOids(), and CSeqDB::SetIterationRange().

◆ BOOST_AUTO_TEST_CASE() [16/117]

BOOST_AUTO_TEST_CASE ( ExpertIdBounds )

Definition at line 2267 of file seqdb_unit_test.cpp.

References count, CSeqDB::eProtein, and nr().

◆ BOOST_AUTO_TEST_CASE() [17/117]

BOOST_AUTO_TEST_CASE ( ExpertIdBoundsNoPig )

Definition at line 2283 of file seqdb_unit_test.cpp.

References count, CSeqDB::eNucleotide, CSeqDBExpert::GetGiBounds(), CSeqDBExpert::GetPigBounds(), and ZERO_GI.

◆ BOOST_AUTO_TEST_CASE() [18/117]

BOOST_AUTO_TEST_CASE ( ExpertNullConstructor )

Definition at line 2166 of file seqdb_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [19/117]

BOOST_AUTO_TEST_CASE ( ExpertRawData )

Definition at line 2194 of file seqdb_unit_test.cpp.

References buffer, CSeqDB::eNucleotide, CSeqDBExpert::GetRawSeqAndAmbig(), CSeqDB::GiToOid(), and s_BufHash().

◆ BOOST_AUTO_TEST_CASE() [20/117]

BOOST_AUTO_TEST_CASE ( ExpertRawDataLength )

Definition at line 2247 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDBExpert::GetRawSeqAndAmbig(), and CSeqDB::GiToOid().

◆ BOOST_AUTO_TEST_CASE() [21/117]

BOOST_AUTO_TEST_CASE ( ExpertRawDataProteinNulls )

Definition at line 2215 of file seqdb_unit_test.cpp.

References A, buffer, CSeqDB::eProtein, CSeqDB::GetNumOIDs(), CSeqDBExpert::GetRawSeqAndAmbig(), CSeqDB::GetSeqLength(), ITERATE, len, and S.

◆ BOOST_AUTO_TEST_CASE() [22/117]

BOOST_AUTO_TEST_CASE ( ExpertTaxInfo )

Definition at line 2172 of file seqdb_unit_test.cpp.

References CSeqDB::GetTaxInfo(), and info.

◆ BOOST_AUTO_TEST_CASE() [23/117]

BOOST_AUTO_TEST_CASE ( ExtractBlastDefline )

Definition at line 4017 of file seqdb_unit_test.cpp.

References CRef< C, Locker >::Empty(), CSeqDB::eNucleotide, CSeqDB::ExtractBlastDefline(), CSeqDB::GetBioseq(), CSeqDB::GiToOid(), CRef< C, Locker >::NotEmpty(), and CBioseq_Base::ResetDescr().

◆ BOOST_AUTO_TEST_CASE() [24/117]

BOOST_AUTO_TEST_CASE ( FilteredHeaders )

Definition at line 3520 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CBlast_def_line_set_Base::Get(), CSeqDB::GetHdr(), and CSeqDB::PigToOid().

◆ BOOST_AUTO_TEST_CASE() [25/117]

BOOST_AUTO_TEST_CASE ( FindGnomonIds )

Definition at line 4039 of file seqdb_unit_test.cpp.

References CSeqDB::AccessionToOids(), CSeqDB::eProtein, i, CSeqDB::SeqidToOid(), and CSeqDB::SeqidToOids().

◆ BOOST_AUTO_TEST_CASE() [26/117]

BOOST_AUTO_TEST_CASE ( GetAmbigSeqAllocN )

Definition at line 438 of file seqdb_unit_test.cpp.

References eMalloc, eNew, CSeqDB::eNucleotide, free(), CSeqDB::GetAmbigSeqAlloc(), kSeqDBNuclBlastNA8, kSeqDBNuclNcbiNA8, and s_BufHash().

◆ BOOST_AUTO_TEST_CASE() [27/117]

BOOST_AUTO_TEST_CASE ( GetAmbigSeqAllocP )

Definition at line 467 of file seqdb_unit_test.cpp.

References eMalloc, eNew, CSeqDB::eProtein, free(), CSeqDB::GetAmbigSeqAlloc(), kSeqDBNuclBlastNA8, kSeqDBNuclNcbiNA8, and s_BufHash().

◆ BOOST_AUTO_TEST_CASE() [28/117]

BOOST_AUTO_TEST_CASE ( GetAmbigSeqN )

Definition at line 496 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::GetAmbigSeq(), kSeqDBNuclBlastNA8, kSeqDBNuclNcbiNA8, CSeqDB::RetAmbigSeq(), and s_BufHash().

◆ BOOST_AUTO_TEST_CASE() [29/117]

BOOST_AUTO_TEST_CASE ( GetAmbigSeqP )

Definition at line 515 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::GetAmbigSeq(), kSeqDBNuclBlastNA8, kSeqDBNuclNcbiNA8, CSeqDB::RetAmbigSeq(), and s_BufHash().

◆ BOOST_AUTO_TEST_CASE() [30/117]

BOOST_AUTO_TEST_CASE ( GetBioseqN )

Definition at line 534 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, expected, GetBioseq(), and s_Stringify().

◆ BOOST_AUTO_TEST_CASE() [31/117]

BOOST_AUTO_TEST_CASE ( GetBioseqP )

Definition at line 577 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, expected, GetBioseq(), and s_Stringify().

◆ BOOST_AUTO_TEST_CASE() [32/117]

BOOST_AUTO_TEST_CASE ( GetHdrN )

Definition at line 619 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, expected, and s_Stringify().

◆ BOOST_AUTO_TEST_CASE() [33/117]

BOOST_AUTO_TEST_CASE ( GetHdrP )

Definition at line 641 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, expected, and s_Stringify().

◆ BOOST_AUTO_TEST_CASE() [34/117]

BOOST_AUTO_TEST_CASE ( GetLeafTaxIDs_gi_to_taxid_set )

Definition at line 1777 of file seqdb_unit_test.cpp.

References set< Key, Compare >::begin(), BEGIN, map_checker< Container >::empty(), set< Key, Compare >::end(), END, CSeqDB::eProtein, CSeqDB::GetLeafTaxIDs(), CSeqDB::GiToOid(), set< Key, Compare >::insert(), ncbi::grid::netcache::search::fields::size, map_checker< Container >::size(), and tax1.

◆ BOOST_AUTO_TEST_CASE() [35/117]

BOOST_AUTO_TEST_CASE ( GetLeafTaxIDs_vector_of_taxids )

Definition at line 1990 of file seqdb_unit_test.cpp.

References BEGIN, END, CSeqDB::eProtein, CSeqDB::GetLeafTaxIDs(), CSeqDB::GiToOid(), ct::sort(), and tax1.

◆ BOOST_AUTO_TEST_CASE() [36/117]

BOOST_AUTO_TEST_CASE ( GetLenHighOID )

Definition at line 1139 of file seqdb_unit_test.cpp.

References CSeqDB::eFilteredAll, CSeqDB::eProtein, CSeqDB::GetSeqLength(), CSeqDB::GetTotals(), and len.

◆ BOOST_AUTO_TEST_CASE() [37/117]

BOOST_AUTO_TEST_CASE ( GetLenNegOID )

Definition at line 1161 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::GetSeqLength(), and len.

◆ BOOST_AUTO_TEST_CASE() [38/117]

BOOST_AUTO_TEST_CASE ( GetSeqData_Nucleotide )

Definition at line 3122 of file seqdb_unit_test.cpp.

References CRef< C, Locker >::Empty(), CSeqDB::eNucleotide, and CSeqDB::GetSeqData().

◆ BOOST_AUTO_TEST_CASE() [39/117]

BOOST_AUTO_TEST_CASE ( GetSeqData_Protein )

Definition at line 3115 of file seqdb_unit_test.cpp.

References CRef< C, Locker >::Empty(), CSeqDB::eProtein, and CSeqDB::GetSeqData().

◆ BOOST_AUTO_TEST_CASE() [40/117]

BOOST_AUTO_TEST_CASE ( GetSeqHighOID )

Definition at line 1180 of file seqdb_unit_test.cpp.

References buffer, CSeqDB::eFilteredAll, CSeqDB::eProtein, CSeqDB::GetSequence(), CSeqDB::GetTotals(), and len.

◆ BOOST_AUTO_TEST_CASE() [41/117]

BOOST_AUTO_TEST_CASE ( GetSeqIDsN )

Definition at line 663 of file seqdb_unit_test.cpp.

References cnt, CSeqDB::eNucleotide, CSeqDB::GetSeqIDs(), i, s_BufHash(), and s_Stringify().

◆ BOOST_AUTO_TEST_CASE() [42/117]

BOOST_AUTO_TEST_CASE ( GetSeqIDsP )

Definition at line 688 of file seqdb_unit_test.cpp.

References cnt, CSeqDB::eProtein, CSeqDB::GetSeqIDs(), i, s_BufHash(), and s_Stringify().

◆ BOOST_AUTO_TEST_CASE() [43/117]

BOOST_AUTO_TEST_CASE ( GetSeqLength )

Definition at line 713 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::eProtein, and CSeqDB::GetSeqLength().

◆ BOOST_AUTO_TEST_CASE() [44/117]

BOOST_AUTO_TEST_CASE ( GetSeqLengthApprox )

Definition at line 738 of file seqdb_unit_test.cpp.

References CSeqDB::eFilteredAll, CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::GetSeqLength(), CSeqDB::GetSeqLengthApprox(), CSeqDB::GetTotals(), i, len, and s_ApproxEqual().

◆ BOOST_AUTO_TEST_CASE() [45/117]

BOOST_AUTO_TEST_CASE ( GetSeqNegOID )

Definition at line 1204 of file seqdb_unit_test.cpp.

References buffer, CSeqDB::eProtein, CSeqDB::GetSequence(), and len.

◆ BOOST_AUTO_TEST_CASE() [46/117]

BOOST_AUTO_TEST_CASE ( GetSequenceAsString )

Definition at line 3163 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::eProtein, N, P, and prot.

◆ BOOST_AUTO_TEST_CASE() [47/117]

BOOST_AUTO_TEST_CASE ( GetSequenceN )

Definition at line 785 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::GetSequence(), CSeqDB::RetSequence(), and s_BufHash().

◆ BOOST_AUTO_TEST_CASE() [48/117]

BOOST_AUTO_TEST_CASE ( GetSequenceP )

Definition at line 799 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::GetSequence(), CSeqDB::RetSequence(), and s_BufHash().

◆ BOOST_AUTO_TEST_CASE() [49/117]

BOOST_AUTO_TEST_CASE ( GetTaxIDs_gi_to_taxid )

Definition at line 1732 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::GetTaxIDs(), CSeqDB::GiToOid(), map_checker< Container >::size(), and tax1.

◆ BOOST_AUTO_TEST_CASE() [50/117]

BOOST_AUTO_TEST_CASE ( GetTaxIDs_vector_of_taxids )

Definition at line 1854 of file seqdb_unit_test.cpp.

References BEGIN, END, CSeqDB::eProtein, CSeqDB::GetTaxIDs(), CSeqDB::GiToOid(), ct::sort(), and tax1.

◆ BOOST_AUTO_TEST_CASE() [51/117]

BOOST_AUTO_TEST_CASE ( GiListInOidRangeIteration )

Definition at line 2075 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::eOidList, CSeqDB::GetNextOIDChunk(), and CSeqDB::SetIterationRange().

◆ BOOST_AUTO_TEST_CASE() [52/117]

BOOST_AUTO_TEST_CASE ( GiListOidRange )

Definition at line 1483 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::eProtein, CSeqDB::GetSeqIDs(), and ITERATE.

◆ BOOST_AUTO_TEST_CASE() [53/117]

BOOST_AUTO_TEST_CASE ( GiLists )

Definition at line 1346 of file seqdb_unit_test.cpp.

References dbname(), CSeqDB::eNucleotide, CSeqDB::eProtein, ITERATE, and names.

◆ BOOST_AUTO_TEST_CASE() [54/117]

BOOST_AUTO_TEST_CASE ( HashToOid )

Definition at line 3416 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDBExpert::GetSequenceHash(), CSeqDBExpert::HashToOids(), and ITERATE.

◆ BOOST_AUTO_TEST_CASE() [55/117]

BOOST_AUTO_TEST_CASE ( IntersectionGiList )

Definition at line 2365 of file seqdb_unit_test.cpp.

References CSeqDBGiList::FindGi(), GI_CONST, GI_FROM, and i.

◆ BOOST_AUTO_TEST_CASE() [56/117]

BOOST_AUTO_TEST_CASE ( IntersectionNegGiList )

Definition at line 2406 of file seqdb_unit_test.cpp.

References CSeqDBNegativeList::FindGi(), CSeqDBGiList::FindGi(), CSeqDBGiList::GetKey(), CSeqDBGiList::GetNumGis(), GI_CONST, GI_FROM, i, int, and CSeqDBNegativeList::SetGiList().

◆ BOOST_AUTO_TEST_CASE() [57/117]

BOOST_AUTO_TEST_CASE ( InvalidPath )

Definition at line 335 of file seqdb_unit_test.cpp.

References CSeqDB::eFilteredAll, CSeqDB::eProtein, and CSeqDB::GetTotals().

◆ BOOST_AUTO_TEST_CASE() [58/117]

BOOST_AUTO_TEST_CASE ( InvalidSeqType )

Definition at line 310 of file seqdb_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [59/117]

BOOST_AUTO_TEST_CASE ( IsBinaryGiList_EmptyFile )

Definition at line 1595 of file seqdb_unit_test.cpp.

References SeqDB_IsBinaryGiList().

◆ BOOST_AUTO_TEST_CASE() [60/117]

BOOST_AUTO_TEST_CASE ( IsBinaryGiList_False )

Definition at line 1589 of file seqdb_unit_test.cpp.

References SeqDB_IsBinaryGiList().

◆ BOOST_AUTO_TEST_CASE() [61/117]

BOOST_AUTO_TEST_CASE ( IsBinaryGiList_InvalidFile )

Definition at line 1601 of file seqdb_unit_test.cpp.

References DEV_NULL, and SeqDB_IsBinaryGiList().

◆ BOOST_AUTO_TEST_CASE() [62/117]

BOOST_AUTO_TEST_CASE ( IsBinaryGiList_True )

Definition at line 1584 of file seqdb_unit_test.cpp.

References SeqDB_IsBinaryGiList().

◆ BOOST_AUTO_TEST_CASE() [63/117]

BOOST_AUTO_TEST_CASE ( MaskDataColumn )

Definition at line 3807 of file seqdb_unit_test.cpp.

References eBlast_filter_program_repeat, eBlast_filter_program_seg, CSeqDB::eProtein, CSeqDB::GetAvailableMaskAlgorithms(), CSeqDB::GetMaskAlgorithmDetails(), CSeqDB::GetNumOIDs(), kCount(), and kEmptyStr.

◆ BOOST_AUTO_TEST_CASE() [64/117]

BOOST_AUTO_TEST_CASE ( MultiTaxidBlastDefLine )

Definition at line 4121 of file seqdb_unit_test.cpp.

References set< Key, Compare >::begin(), set< Key, Compare >::end(), CBlast_def_line::GetLeafTaxIds(), set< Key, Compare >::insert(), CBlast_def_line_Base::IsSetLinks(), CBlast_def_line_Base::IsSetTaxid(), and CBlast_def_line::SetLeafTaxIds().

◆ BOOST_AUTO_TEST_CASE() [65/117]

BOOST_AUTO_TEST_CASE ( NegativeGiList )

Definition at line 3259 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::GetNumSeqs(), CSeqDB::GetSeqIDs(), CSeqDB::GetTotalLength(), CSeqDB::GiToOid(), ITERATE, ok, s_MapAllGis(), s_ModifyMap(), and map_checker< Container >::size().

◆ BOOST_AUTO_TEST_CASE() [66/117]

BOOST_AUTO_TEST_CASE ( NegativeListNt )

Definition at line 3357 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::GetGis(), CSeqDB::GetNumSeqs(), CSeqDB::GiToOid(), and int.

◆ BOOST_AUTO_TEST_CASE() [67/117]

BOOST_AUTO_TEST_CASE ( NegativeListSwissprot )

Definition at line 3388 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::GetNumSeqs(), CSeqDB::GetTotalLength(), len, CSeqDB::OidToPig(), CSeqDB::PigToOid(), and CSeqDBNegativeList::SetPigList().

◆ BOOST_AUTO_TEST_CASE() [68/117]

BOOST_AUTO_TEST_CASE ( NrAndSwissProt )

Definition at line 812 of file seqdb_unit_test.cpp.

References CSeqDB::eFilteredAll, CSeqDB::eProtein, CSeqDB::eUnfilteredAll, CSeqDB::GetMaxLength(), CSeqDB::GetTotals(), and nr().

◆ BOOST_AUTO_TEST_CASE() [69/117]

BOOST_AUTO_TEST_CASE ( NuclOldTest )

Definition at line 3645 of file seqdb_unit_test.cpp.

References CSeqDB::eUnknown, and s_CheckIdLookup().

◆ BOOST_AUTO_TEST_CASE() [70/117]

BOOST_AUTO_TEST_CASE ( NuclTest )

Definition at line 3664 of file seqdb_unit_test.cpp.

References CSeqDB::eUnknown, and s_CheckIdLookup().

◆ BOOST_AUTO_TEST_CASE() [71/117]

BOOST_AUTO_TEST_CASE ( Offset2OidBadOffset )

Definition at line 1225 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::eUnfilteredAll, and nr().

◆ BOOST_AUTO_TEST_CASE() [72/117]

BOOST_AUTO_TEST_CASE ( Offset2OidBadOid )

Definition at line 1247 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::eUnfilteredAll, and nr().

◆ BOOST_AUTO_TEST_CASE() [73/117]

BOOST_AUTO_TEST_CASE ( Offset2OidMonotony )

Definition at line 1268 of file seqdb_unit_test.cpp.

References dbname(), CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::eUnfilteredAll, fabs, CSeqDB::GetOidAtOffset(), CSeqDB::GetTotals(), and i.

◆ BOOST_AUTO_TEST_CASE() [74/117]

BOOST_AUTO_TEST_CASE ( OidAndGiLists )

Definition at line 3956 of file seqdb_unit_test.cpp.

References SDbSumInfo::Compare(), SDbSumInfo::CompareSelf(), CSeqDB::eProtein, and nr().

◆ BOOST_AUTO_TEST_CASE() [75/117]

BOOST_AUTO_TEST_CASE ( OidRanges )

Definition at line 1367 of file seqdb_unit_test.cpp.

References count, dbname(), eAll, eEND, eOdd, CSeqDB::eOidList, CSeqDB::eProtein, first(), CSeqDB::GetNextOIDChunk(), i, int, ITERATE, mask, s_MaskingTest(), s_TestMaskingLimits(), and s_ToString().

◆ BOOST_AUTO_TEST_CASE() [76/117]

BOOST_AUTO_TEST_CASE ( OidRewriting )

Definition at line 3129 of file seqdb_unit_test.cpp.

References count, CSeq_id_Base::e_General, CSeqDB::eNucleotide, CSeq_id_Base::GetGeneral(), CObject_id_Base::GetId(), CSeqDB::GetSeqIDs(), and CDbtag_Base::GetTag().

◆ BOOST_AUTO_TEST_CASE() [77/117]

BOOST_AUTO_TEST_CASE ( OidToGiLookup )

Definition at line 2808 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::GetSeqGI(), and CSeqDB::GiToOid().

◆ BOOST_AUTO_TEST_CASE() [78/117]

BOOST_AUTO_TEST_CASE ( OpenWithBLASTDBEnv )

Definition at line 1329 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, and CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [79/117]

BOOST_AUTO_TEST_CASE ( OpenWithoutBLASTDBEnv )

Definition at line 1337 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, and CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [80/117]

BOOST_AUTO_TEST_CASE ( PartialSequences )

Definition at line 2061 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, and s_TestPartialAmbig().

◆ BOOST_AUTO_TEST_CASE() [81/117]

BOOST_AUTO_TEST_CASE ( PathDelimiters )

Definition at line 272 of file seqdb_unit_test.cpp.

References CSeqDB::eFilteredAll, CSeqDB::eProtein, and CSeqDB::GetTotals().

◆ BOOST_AUTO_TEST_CASE() [82/117]

BOOST_AUTO_TEST_CASE ( PdbIdWithChain )

Definition at line 3683 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, and nr().

◆ BOOST_AUTO_TEST_CASE() [83/117]

BOOST_AUTO_TEST_CASE ( PigListSwissprot )

Definition at line 4294 of file seqdb_unit_test.cpp.

References CSeqDB::AccessionToOids(), CSeqDBGiList::AddPig(), CSeqDB::CheckOrFindOID(), CSeqDB::eProtein, CSeqDB::GetNumSeqs(), CSeqDBGiList::GetPigList(), CSeqDB::GetSeqIDs(), i, not_found, CSeqDB::SeqidToOid(), and CSeqDBNegativeList::SetPigList().

◆ BOOST_AUTO_TEST_CASE() [84/117]

BOOST_AUTO_TEST_CASE ( ProtOldTest )

Definition at line 3596 of file seqdb_unit_test.cpp.

References CSeqDB::eUnknown, and s_CheckIdLookup().

◆ BOOST_AUTO_TEST_CASE() [85/117]

BOOST_AUTO_TEST_CASE ( ProtTest )

Definition at line 3619 of file seqdb_unit_test.cpp.

References CSeqDB::eUnknown, and s_CheckIdLookup().

◆ BOOST_AUTO_TEST_CASE() [86/117]

BOOST_AUTO_TEST_CASE ( ResolveDbPath )

Definition at line 2318 of file seqdb_unit_test.cpp.

References ITERATE, and SeqDB_ResolveDbPath().

◆ BOOST_AUTO_TEST_CASE() [87/117]

BOOST_AUTO_TEST_CASE ( RestartWithVolumes )

Definition at line 4012 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [88/117]

BOOST_AUTO_TEST_CASE ( SeqIdList )

Definition at line 2762 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::eProtein, CBlast_def_line_set_Base::Get(), CSeqDB::GetHdr(), i, NULL, and str().

◆ BOOST_AUTO_TEST_CASE() [89/117]

BOOST_AUTO_TEST_CASE ( SeqIdListAndGiList )

Definition at line 2828 of file seqdb_unit_test.cpp.

References CSeq_id::AsFastaString(), CSeqDB::CheckOrFindOID(), set< Key, Compare >::empty(), set< Key, Compare >::end(), CSeqDB::eProtein, set< Key, Compare >::erase(), set< Key, Compare >::find(), CSeqDB::GetSeqIDs(), i, set< Key, Compare >::insert(), ITERATE, NULL, SeqDB_SimplifyAccession(), and str().

◆ BOOST_AUTO_TEST_CASE() [90/117]

BOOST_AUTO_TEST_CASE ( SeqidToOid )

Definition at line 2113 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, ITERATE, CSeqDB::SeqidToOid(), and CSeqDB::SeqidToOids().

◆ BOOST_AUTO_TEST_CASE() [91/117]

BOOST_AUTO_TEST_CASE ( SharedMemoryMaps )

Definition at line 2706 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::GetSequence(), and CSeqDB::RetSequence().

◆ BOOST_AUTO_TEST_CASE() [92/117]

BOOST_AUTO_TEST_CASE ( SingleTaxidBlastDefLine )

Definition at line 4142 of file seqdb_unit_test.cpp.

References set< Key, Compare >::begin(), set< Key, Compare >::end(), expected, CBlast_def_line::GetLeafTaxIds(), CBlast_def_line_Base::GetTaxid(), CBlast_def_line_Base::IsSetLinks(), CBlast_def_line_Base::IsSetTaxid(), kTaxid, CBlast_def_line::SetLeafTaxIds(), CBlast_def_line_Base::SetTaxid(), set< Key, Compare >::size(), TAX_ID_CONST, and ZERO_TAX_ID.

◆ BOOST_AUTO_TEST_CASE() [93/117]

BOOST_AUTO_TEST_CASE ( StringIdentSearch )

Definition at line 888 of file seqdb_unit_test.cpp.

References ArraySize(), set< Key, Compare >::begin(), set< Key, Compare >::end(), CSeqDB::eProtein, i, set< Key, Compare >::insert(), ITERATE, kDb(), and nr().

◆ BOOST_AUTO_TEST_CASE() [94/117]

BOOST_AUTO_TEST_CASE ( SummaryDataN )

Definition at line 355 of file seqdb_unit_test.cpp.

References dbname(), CSeqDB::eFilteredRange, CSeqDB::eNucleotide, CSeqDB::eUnfilteredAll, CSeqDB::GetDBNameList(), CSeqDB::GetMaxLength(), CSeqDB::GetSequenceType(), CSeqDB::GetTitle(), CSeqDB::GetTotals(), CSeqDB::SetIterationRange(), and U.

◆ BOOST_AUTO_TEST_CASE() [95/117]

BOOST_AUTO_TEST_CASE ( SummaryDataP )

Definition at line 415 of file seqdb_unit_test.cpp.

References dbname(), CSeqDB::eFilteredAll, CSeqDB::eProtein, CSeqDB::eUnfilteredAll, CSeqDB::GetDBNameList(), CSeqDB::GetMaxLength(), CSeqDB::GetSequenceType(), CSeqDB::GetTitle(), and CSeqDB::GetTotals().

◆ BOOST_AUTO_TEST_CASE() [96/117]

BOOST_AUTO_TEST_CASE ( TaxFilterWithGiListDB )

Definition at line 4443 of file seqdb_unit_test.cpp.

References CSeqDBGiList::AddTaxIds(), CSeqDB::eFilteredAll, CSeqDB::eNucleotide, CSeqDB::GetTotals(), t, and TAX_ID_CONST.

◆ BOOST_AUTO_TEST_CASE() [97/117]

BOOST_AUTO_TEST_CASE ( Test_Mix_GI_SeqId_List_AliasFile )

Definition at line 4268 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::eProtein, and i.

◆ BOOST_AUTO_TEST_CASE() [98/117]

BOOST_AUTO_TEST_CASE ( Test_Mix_User_SeqIdList_AliasFile )

Definition at line 4282 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::eProtein, CSeqDBFileGiList::eSiList, and i.

◆ BOOST_AUTO_TEST_CASE() [99/117]

BOOST_AUTO_TEST_CASE ( Test_Multi_SeqIdList_AliasFile )

Definition at line 4257 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), and CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [100/117]

BOOST_AUTO_TEST_CASE ( Test_SeqIdList_AliasFile )

Definition at line 4224 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), and CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [101/117]

BOOST_AUTO_TEST_CASE ( Test_SeqIdList_FilteredID )

Definition at line 4235 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::GetSeqIDs(), ITERATE, and kEmptyStr.

◆ BOOST_AUTO_TEST_CASE() [102/117]

BOOST_AUTO_TEST_CASE ( TestDiskUsage )

Definition at line 4032 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, and CSeqDB::GetDiskUsage().

◆ BOOST_AUTO_TEST_CASE() [103/117]

BOOST_AUTO_TEST_CASE ( TestMemoryMapFile )

Definition at line 4459 of file seqdb_unit_test.cpp.

References CSeqDBAtlas::ChangeOpenedFilseCount(), CSeqDBAtlas::e_MaxFileDescritors, CSeqDBAtlas::eFileCounterIncrement, eGiId, CSeqDBAtlas::GetOpenedFilseCount(), i, and CSeqDBIsam::UnLease().

◆ BOOST_AUTO_TEST_CASE() [104/117]

BOOST_AUTO_TEST_CASE ( TestMemoryMapFile_MT )

Definition at line 4495 of file seqdb_unit_test.cpp.

References CSeqDBAtlas::GetOpenedFilseCount(), and i.

◆ BOOST_AUTO_TEST_CASE() [105/117]

BOOST_AUTO_TEST_CASE ( TestOidNotFoundWithUserAliasFileAndGiList )

Definition at line 4073 of file seqdb_unit_test.cpp.

References CSeqDB::AccessionToOids(), CFileDeleteAtExit::Add(), CSeqDB::eProtein, CTmpFile::GetFileName(), and U.

◆ BOOST_AUTO_TEST_CASE() [106/117]

BOOST_AUTO_TEST_CASE ( TestResetInternalChunkBookmark )

Definition at line 2136 of file seqdb_unit_test.cpp.

References CSeqDB::eOidRange, CSeqDB::eProtein, CSeqDB::GetNextOIDChunk(), CSeqDB::ResetInternalChunkBookmark(), and CSeqDB::SetIterationRange().

◆ BOOST_AUTO_TEST_CASE() [107/117]

BOOST_AUTO_TEST_CASE ( TestSpaceInDbName )

Definition at line 4108 of file seqdb_unit_test.cpp.

References SDbSumInfo::CompareSelf(), and CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [108/117]

BOOST_AUTO_TEST_CASE ( TestTaxIdsLookup )

Definition at line 4514 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, CSeqDB::GetTaxIdsForAccession(), and CSeqDB::GetTaxIdsForSeqId().

◆ BOOST_AUTO_TEST_CASE() [109/117]

BOOST_AUTO_TEST_CASE ( TestTaxIdsLookup_v4 )

Definition at line 4541 of file seqdb_unit_test.cpp.

References CSeqDB::eProtein, and CSeqDB::GetTaxIdsForAccession().

◆ BOOST_AUTO_TEST_CASE() [110/117]

BOOST_AUTO_TEST_CASE ( TextUserGiList )

Definition at line 1626 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), and CSeqDB::eProtein.

◆ BOOST_AUTO_TEST_CASE() [111/117]

BOOST_AUTO_TEST_CASE ( TotalLengths )

Definition at line 3194 of file seqdb_unit_test.cpp.

References CSeqDB::eNucleotide, CSeqDB::GetNumSeqsStats(), CSeqDB::GetTotalLengthStats(), and local.

◆ BOOST_AUTO_TEST_CASE() [112/117]

BOOST_AUTO_TEST_CASE ( TranslateIdents )

Definition at line 838 of file seqdb_unit_test.cpp.

References ArraySize(), CSeqDB::eProtein, i, and nr().

◆ BOOST_AUTO_TEST_CASE() [113/117]

BOOST_AUTO_TEST_CASE ( TwoGiListsOneVolume )

Definition at line 1692 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::eNucleotide, CSeqDB::FindVolumePaths(), CSeqDB::GetGis(), i, int, CRef< C, Locker >::Reset(), ncbi::grid::netcache::search::fields::size, and ct::sort().

◆ BOOST_AUTO_TEST_CASE() [114/117]

BOOST_AUTO_TEST_CASE ( UserDefinedColumns )

Definition at line 3698 of file seqdb_unit_test.cpp.

References columns, count, CR, map_checker< Container >::end(), CSeqDB::eProtein, map_checker< Container >::find(), CSeqDB::FindVolumePaths(), CSeqDB::GetColumnBlob(), CSeqDB::GetColumnId(), CSeqDB::GetColumnMetaData(), CSeqDB::GetColumnValue(), CSeqDB::GetNumOIDs(), CSeqDB::ListColumns(), min(), map_checker< Container >::size(), and CBlastDbBlob::Str().

◆ BOOST_AUTO_TEST_CASE() [115/117]

BOOST_AUTO_TEST_CASE ( UserSeqIdList )

Definition at line 1642 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::eProtein, and CSeqDBFileGiList::eSiList.

◆ BOOST_AUTO_TEST_CASE() [116/117]

BOOST_AUTO_TEST_CASE ( ValidPath )

Definition at line 325 of file seqdb_unit_test.cpp.

References CSeqDB::eFilteredAll, CSeqDB::eProtein, and CSeqDB::GetTotals().

◆ BOOST_AUTO_TEST_CASE() [117/117]

BOOST_AUTO_TEST_CASE ( VersionedSparseId )

Definition at line 3786 of file seqdb_unit_test.cpp.

References CSeqDB::AccessionToOids(), and CSeqDB::eNucleotide.

◆ s_ApproxEqual()

template<class NUM , class DIF >

void s_ApproxEqual	(	NUM	a,
		NUM	b,
		DIF	epsilon,
		int	lineno
	)

Definition at line 212 of file seqdb_unit_test.cpp.

References a, b, epsilon, and lineno.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_BufHash()

static Uint4 s_BufHash	(	const char *	buf_in,
		Uint4	length,
		Uint4	start = `1`
	)

static

Definition at line 228 of file seqdb_unit_test.cpp.

References buf, and i.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_CheckIdLookup()

static void s_CheckIdLookup	(	CSeqDB &	db,
		const string &	acc,
		size_t	exp_oids,
		size_t	exp_size
	)

static

Definition at line 3556 of file seqdb_unit_test.cpp.

References CSeqDB::AccessionToOids(), NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, CSeqDB::GetBioseq(), ITERATE, msg(), CFastaOstream::SetWidth(), ct::sort(), NStr::Split(), string, and CFastaOstream::Write().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_DbHasOID()

static bool s_DbHasOID	(	CSeqDB &	db,
		int &	count,
		int	oid
	)

static

Definition at line 2614 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), and count.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_MapAllGis()

static void s_MapAllGis	(	CSeqDB &	db,
		map< int, int > &	m,
		int	change,
		int &	total
	)

static

Definition at line 3240 of file seqdb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::GetGis(), GI_TO, ITERATE, and s_ModifyMap().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_MaskingTest()

static bool s_MaskingTest	(	EMaskingType	mask,
		unsigned	oid
	)

static

Definition at line 127 of file seqdb_unit_test.cpp.

References eAll, eEven, eOdd, ePrime, and mask.

Referenced by BOOST_AUTO_TEST_CASE(), and s_TestMaskingLimits().

◆ s_ModifyMap()

static void s_ModifyMap	(	map< int, int > &	m,
		int	key,
		int	c,
		int &	total
	)

static

Definition at line 3229 of file seqdb_unit_test.cpp.

References map_checker< Container >::erase(), and ncbi::grid::netcache::search::fields::key.

Referenced by BOOST_AUTO_TEST_CASE(), and s_MapAllGis().

◆ s_Stringify()

template<class ASNOBJ >

string s_Stringify ( CRef< ASNOBJ > a )

Definition at line 247 of file seqdb_unit_test.cpp.

References a, and MSerial_AsnText.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_TestMaskingLimits()

static void s_TestMaskingLimits	(	EMaskingType	mask,
		unsigned	first,
		unsigned	last,
		unsigned	lowest,
		unsigned	highest,
		unsigned	count
	)

static

Definition at line 167 of file seqdb_unit_test.cpp.

References count, first(), i, last(), mask, and s_MaskingTest().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_TestPartialAmbig()

static void s_TestPartialAmbig	(	CSeqDB &	db,
		TGi	nt_gi
	)

static

Definition at line 100 of file seqdb_unit_test.cpp.

References CSeqDB::GetSeqLength(), CSeqDB::GiToOid(), i, msg(), and s_TestPartialAmbigRange().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_TestPartialAmbigRange()

static void s_TestPartialAmbigRange	(	CSeqDB &	db,
		int	oid,
		int	begin,
		int	end
	)

static

Definition at line 77 of file seqdb_unit_test.cpp.

References CSeqDB::GetAmbigSeq(), kSeqDBNuclNcbiNA8, CSeqDB::RetAmbigSeq(), s_ToString(), and whole.

Referenced by s_TestPartialAmbig().

◆ s_ToString()

template<class A , class B , class C , class D , class E >

string s_ToString	(	const A &	a,
		const B &	b,
		const C &	c,
		const D &	d,
		const E &	e
	)

Definition at line 66 of file seqdb_unit_test.cpp.

References a, and b.

Referenced by BOOST_AUTO_TEST_CASE(), and s_TestPartialAmbigRange().

◆ USING_SCOPE()

USING_SCOPE ( objects )

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 60 of file seqdb_unit_test.cpp.

Classes

Macros

Enumerations

Functions

Variables

Macro Definition Documentation

◆ BEGIN

◆ DEV_NULL

◆ END

◆ NCBI_TEST_APPLICATION

Enumeration Type Documentation

◆ EMaskingType

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/117]

◆ BOOST_AUTO_TEST_CASE() [2/117]

◆ BOOST_AUTO_TEST_CASE() [3/117]

◆ BOOST_AUTO_TEST_CASE() [4/117]

◆ BOOST_AUTO_TEST_CASE() [5/117]

◆ BOOST_AUTO_TEST_CASE() [6/117]

◆ BOOST_AUTO_TEST_CASE() [7/117]

◆ BOOST_AUTO_TEST_CASE() [8/117]

◆ BOOST_AUTO_TEST_CASE() [9/117]

◆ BOOST_AUTO_TEST_CASE() [10/117]

◆ BOOST_AUTO_TEST_CASE() [11/117]

◆ BOOST_AUTO_TEST_CASE() [12/117]

◆ BOOST_AUTO_TEST_CASE() [13/117]

◆ BOOST_AUTO_TEST_CASE() [14/117]

◆ BOOST_AUTO_TEST_CASE() [15/117]

◆ BOOST_AUTO_TEST_CASE() [16/117]

◆ BOOST_AUTO_TEST_CASE() [17/117]

◆ BOOST_AUTO_TEST_CASE() [18/117]

◆ BOOST_AUTO_TEST_CASE() [19/117]

◆ BOOST_AUTO_TEST_CASE() [20/117]

◆ BOOST_AUTO_TEST_CASE() [21/117]

◆ BOOST_AUTO_TEST_CASE() [22/117]

◆ BOOST_AUTO_TEST_CASE() [23/117]

◆ BOOST_AUTO_TEST_CASE() [24/117]

◆ BOOST_AUTO_TEST_CASE() [25/117]

◆ BOOST_AUTO_TEST_CASE() [26/117]

◆ BOOST_AUTO_TEST_CASE() [27/117]

◆ BOOST_AUTO_TEST_CASE() [28/117]

◆ BOOST_AUTO_TEST_CASE() [29/117]

◆ BOOST_AUTO_TEST_CASE() [30/117]

◆ BOOST_AUTO_TEST_CASE() [31/117]

◆ BOOST_AUTO_TEST_CASE() [32/117]

◆ BOOST_AUTO_TEST_CASE() [33/117]

◆ BOOST_AUTO_TEST_CASE() [34/117]

◆ BOOST_AUTO_TEST_CASE() [35/117]

◆ BOOST_AUTO_TEST_CASE() [36/117]

◆ BOOST_AUTO_TEST_CASE() [37/117]

◆ BOOST_AUTO_TEST_CASE() [38/117]

◆ BOOST_AUTO_TEST_CASE() [39/117]

◆ BOOST_AUTO_TEST_CASE() [40/117]

◆ BOOST_AUTO_TEST_CASE() [41/117]

◆ BOOST_AUTO_TEST_CASE() [42/117]

◆ BOOST_AUTO_TEST_CASE() [43/117]

◆ BOOST_AUTO_TEST_CASE() [44/117]

◆ BOOST_AUTO_TEST_CASE() [45/117]

◆ BOOST_AUTO_TEST_CASE() [46/117]

◆ BOOST_AUTO_TEST_CASE() [47/117]

◆ BOOST_AUTO_TEST_CASE() [48/117]

◆ BOOST_AUTO_TEST_CASE() [49/117]

◆ BOOST_AUTO_TEST_CASE() [50/117]

◆ BOOST_AUTO_TEST_CASE() [51/117]

◆ BOOST_AUTO_TEST_CASE() [52/117]

◆ BOOST_AUTO_TEST_CASE() [53/117]

◆ BOOST_AUTO_TEST_CASE() [54/117]

◆ BOOST_AUTO_TEST_CASE() [55/117]

◆ BOOST_AUTO_TEST_CASE() [56/117]

◆ BOOST_AUTO_TEST_CASE() [57/117]

◆ BOOST_AUTO_TEST_CASE() [58/117]

◆ BOOST_AUTO_TEST_CASE() [59/117]

◆ BOOST_AUTO_TEST_CASE() [60/117]

◆ BOOST_AUTO_TEST_CASE() [61/117]

◆ BOOST_AUTO_TEST_CASE() [62/117]

◆ BOOST_AUTO_TEST_CASE() [63/117]

◆ BOOST_AUTO_TEST_CASE() [64/117]

◆ BOOST_AUTO_TEST_CASE() [65/117]

◆ BOOST_AUTO_TEST_CASE() [66/117]

◆ BOOST_AUTO_TEST_CASE() [67/117]