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USING_SCOPE (objects) void s_FetchRawData (CSeqDBExpert &seqdb, int oid, string &sequence, string &ambig) CRef< CSeq_id > s_GiToSeqId (TGi gi) CRef< CSeq_id > s_AccToSeqId (const char *acc) string s_HexDumpText (const string &raw, const vector< int > &layout, int base) string s_HexDumpText (const string &raw, int per, int base) string s_HexDumpFile (const string &fname, const vector< int > &layout, int base) string s_HexDumpFile (const string &fname, int per, int base) static void s_DupIdsBioseq (CWriteDB &w, CSeqDB &s, const TIdList &ids, int cutpoint) static void s_DupIdsRaw (CWriteDB &w, CSeqDBExpert &seqdb, const TIdList &ids) template<class ASNOBJ > void s_Stringify (const ASNOBJ &a, string &s) template<class ASNOBJ > void s_Unstringify (const string &s, ASNOBJ &a) template<class ASNOBJ > CRef< ASNOBJ > s_Duplicate (const ASNOBJ &a) void s_CompareBioseqs (CBioseq &src, CBioseq &dst) void s_TestDatabase (CSeqDBExpert &src, const string &name, const string &title) void s_RemoveFile (const string &f) void s_RemoveFiles (const vector< string > &files) void s_CheckSorted (const string &fname) string s_ExtractLast (const string &data, const string &delim) void s_CheckFiles (const vector< string > &files, bool need_hash=false) void s_WrapUpFiles (const vector< string > &files) void s_WrapUpDb (CWriteDB &db) static void s_DupSequencesTest (const TIdList &ids, bool is_protein, bool raw_data, const string &src_name, const string &dst_name, const string &title, int cutpoint=99) static CRef< CScope > s_GetScope () static void s_BuildIds (TIdList &ids, TGi *gis) static void s_BuildIds (TIdList &ids, const char **gis) CRef< CBioseq > s_FastaStringToBioseq (const string &str, bool protein) static void s_NuclBioseqDupSwitch (int cutpoint) BOOST_AUTO_TEST_CASE (NuclBioseqDupI) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ4) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ8) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ12) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ16) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ20) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ24) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ28) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ32) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ33) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ34) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ35) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ36) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ40) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ44) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ45) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ46) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ47) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ48) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ49) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ50) BOOST_AUTO_TEST_CASE (NuclBioseqDupJ) BOOST_AUTO_TEST_CASE (NuclBioseqDupK) BOOST_AUTO_TEST_CASE (NuclBioseqDup) BOOST_AUTO_TEST_CASE (ProtBioseqDup) BOOST_AUTO_TEST_CASE (EmptyBioseq) BOOST_AUTO_TEST_CASE (BioseqHandle) BOOST_AUTO_TEST_CASE (BioseqHandleAndSeqVectorNonWriteDB) BOOST_AUTO_TEST_CASE (BioseqHandleAndSeqVector) BOOST_AUTO_TEST_CASE (BioseqHandleAndSeqVectorWriteDB) BOOST_AUTO_TEST_CASE (SetPig) BOOST_AUTO_TEST_CASE (MultiVolume) BOOST_AUTO_TEST_CASE (UsPatId) BOOST_AUTO_TEST_CASE (IsamSorting) BOOST_AUTO_TEST_CASE (DuplicateId) BOOST_AUTO_TEST_CASE (HashToOid) BOOST_AUTO_TEST_CASE (MismatchedDb_Bioseq) BOOST_AUTO_TEST_CASE (PDBIdLowerCase) BOOST_AUTO_TEST_CASE (FastaReaderBioseq) BOOST_AUTO_TEST_CASE (BinaryListBuilder) BOOST_AUTO_TEST_CASE (FourAndEightByteTis) void s_WrapUpColumn (CWriteDB_ColumnBuilder &cb) BOOST_AUTO_TEST_CASE (UserDefinedColumns) BOOST_AUTO_TEST_CASE (RegisterMaskingAlgorithms) BOOST_AUTO_TEST_CASE (RegisterVariantsOfSameMaskingAlgorithm) void RegisterTooManyVariantsOfSameMaskingAlgorithm (EBlast_filter_program masking_algo, size_t kMaxNumSupportedAlgorithmVariants) BOOST_AUTO_TEST_CASE (RegisterTooManyVariantsOfDust) BOOST_AUTO_TEST_CASE (RegisterTooManyVariantsOfSeg) BOOST_AUTO_TEST_CASE (RegisterTooManyVariantsOfWindowMasker) BOOST_AUTO_TEST_CASE (RegisterTooManyVariantsOfRepeats) BOOST_AUTO_TEST_CASE (RegisterTooManyVariantsOfOther) BOOST_AUTO_TEST_CASE (MaskDataColumn) BOOST_AUTO_TEST_CASE (DuplicateAlgoId) BOOST_AUTO_TEST_CASE (TooManyAlgoId) BOOST_AUTO_TEST_CASE (UndefinedAlgoID) BOOST_AUTO_TEST_CASE (MaskDataBoundsError) BOOST_AUTO_TEST_CASE (AliasFileGeneration) BOOST_AUTO_TEST_CASE (AliasFileGeneration_SeqIdList) BOOST_AUTO_TEST_CASE (AliasFileGeneration_WithDbListNumVolumes) BOOST_AUTO_TEST_CASE (AliasFileGenerationWithOidRange) BOOST_AUTO_TEST_CASE (AliasFileGeneration_WithDbListAggregateBlastDbs) BOOST_AUTO_TEST_CASE (InvalidAliasFileGeneration_NonExistentDb) BOOST_AUTO_TEST_CASE (InvalidAliasFileGeneration_NonExistentDbAggregation) BOOST_AUTO_TEST_CASE (InvalidAliasFileGeneration_NonExistentMultiVolDbAggregation) BOOST_AUTO_TEST_CASE (InvalidAliasFileGeneration_NoGisInBlastDB) BOOST_AUTO_TEST_CASE (CBuildDatabase_WriteToInvalidPathWindows) BOOST_AUTO_TEST_CASE (CBuildDatabase_WriteToInvalidPathUnix) BOOST_AUTO_TEST_CASE (CWriteDB_SetTaxonomy) BOOST_AUTO_TEST_CASE (CWriteDB_SetTaxonomyFromMap) BOOST_AUTO_TEST_CASE (CWriteDB_SetTaxonomyFromMapLclIds) BOOST_AUTO_TEST_CASE (CBuildDatabase_TestDirectoryCreation) BOOST_AUTO_TEST_CASE (CBuildDatabase_TestBasicDatabaseCreation) BOOST_AUTO_TEST_CASE (CBuildDatabase_TestQuickDatabaseCreation) BOOST_AUTO_TEST_CASE (CBuildDatabase_TestQuickDatabaseCreation_NoIds) BOOST_AUTO_TEST_CASE (CBuildDatabase_WGS_gap) BOOST_AUTO_TEST_CASE (ReadBareIDProtein) BOOST_AUTO_TEST_CASE (ReadMultipleBareIDs) BOOST_AUTO_TEST_CASE (ReadBareIDNucleotide) BOOST_AUTO_TEST_CASE (ReadMixIDsProtein) BOOST_AUTO_TEST_CASE (ReadMultipleMixLongIDs) BOOST_AUTO_TEST_CASE (ReadMixIDNucleotide) BOOST_AUTO_TEST_CASE (CreateV5Seqidlist) BOOST_AUTO_TEST_CASE (ReadMultiSeqIdsDefline) BOOST_AUTO_TEST_CASE (ReadPDBFasta) void s_TestReadPDBAsn1 (CNcbiIfstream &istr, CNcbiIfstream &ref_ids_file, int num_oids) BOOST_AUTO_TEST_CASE (ReadPDBAsn1) BOOST_AUTO_TEST_CASE (LimitProteinDeflines) ◆ BOOST_REQUIRE_CUTPOINT ◆ NCBI_TEST_APPLICATION ◆ TIdList ◆ BOOST_AUTO_TEST_CASE() [1/84] BOOST_AUTO_TEST_CASE ( AliasFileGeneration )Definition at line 2212 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), eDiag_Fatal, CWriteDB::eProtein, NStr::Find(), SAliasFileData::Value::Found(), SAliasFileData::Value::Get(), CTmpFile::GetFileName(), kTitle, SAliasFileData::m_DbList, SAliasFileData::m_FirstOid, SAliasFileData::m_GiList, SAliasFileData::m_LastOid, SAliasFileData::m_Length, SAliasFileData::m_NSeqs, SAliasFileData::m_SeqidList, SAliasFileData::m_TiList, SAliasFileData::m_Title, NPOS, and SetDiagPostLevel().
◆ BOOST_AUTO_TEST_CASE() [2/84] BOOST_AUTO_TEST_CASE ( AliasFileGeneration_SeqIdList )Definition at line 2252 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), eDiag_Fatal, CWriteDB::eProtein, eSeqIdList, NStr::Find(), SAliasFileData::Value::Found(), SAliasFileData::Value::Get(), CTmpFile::GetFileName(), kTitle, SAliasFileData::m_DbList, SAliasFileData::m_FirstOid, SAliasFileData::m_GiList, SAliasFileData::m_LastOid, SAliasFileData::m_Length, SAliasFileData::m_NSeqs, SAliasFileData::m_SeqidList, SAliasFileData::m_TiList, SAliasFileData::m_Title, NPOS, and SetDiagPostLevel().
◆ BOOST_AUTO_TEST_CASE() [3/84] BOOST_AUTO_TEST_CASE ( AliasFileGeneration_WithDbListAggregateBlastDbs )Definition at line 2357 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), eDiag_Fatal, CWriteDB::eNucleotide, NStr::Find(), SAliasFileData::Value::Found(), SAliasFileData::Value::Get(), ITERATE, kEmptyStr, kTitle, SAliasFileData::m_DbList, SAliasFileData::m_FirstOid, SAliasFileData::m_GiList, SAliasFileData::m_LastOid, SAliasFileData::m_Length, SAliasFileData::m_NSeqs, SAliasFileData::m_SeqidList, SAliasFileData::m_TiList, SAliasFileData::m_Title, NPOS, and SetDiagPostLevel().
◆ BOOST_AUTO_TEST_CASE() [4/84] BOOST_AUTO_TEST_CASE ( AliasFileGeneration_WithDbListNumVolumes )Definition at line 2291 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), eDiag_Fatal, CWriteDB::eProtein, NStr::Find(), SAliasFileData::Value::Found(), SAliasFileData::Value::Get(), NStr::IntToString(), kTitle, SAliasFileData::m_DbList, SAliasFileData::m_FirstOid, SAliasFileData::m_GiList, SAliasFileData::m_LastOid, SAliasFileData::m_Length, SAliasFileData::m_NSeqs, SAliasFileData::m_SeqidList, SAliasFileData::m_TiList, SAliasFileData::m_Title, NPOS, and SetDiagPostLevel().
◆ BOOST_AUTO_TEST_CASE() [5/84] BOOST_AUTO_TEST_CASE ( AliasFileGenerationWithOidRange )Definition at line 2322 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), eDiag_Fatal, CWriteDB::eProtein, NStr::Find(), SAliasFileData::Value::Found(), SAliasFileData::Value::Get(), CTmpFile::GetFileName(), CRange_Base::GetFrom(), COpenRange< Position >::GetToOpen(), NStr::IntToString(), kTitle, SAliasFileData::m_DbList, SAliasFileData::m_FirstOid, SAliasFileData::m_GiList, SAliasFileData::m_LastOid, SAliasFileData::m_Length, SAliasFileData::m_NSeqs, SAliasFileData::m_SeqidList, SAliasFileData::m_TiList, SAliasFileData::m_Title, NPOS, and SetDiagPostLevel().
◆ BOOST_AUTO_TEST_CASE() [6/84] BOOST_AUTO_TEST_CASE ( BinaryListBuilder ) ◆ BOOST_AUTO_TEST_CASE() [7/84] BOOST_AUTO_TEST_CASE ( BioseqHandle ) ◆ BOOST_AUTO_TEST_CASE() [8/84] BOOST_AUTO_TEST_CASE ( BioseqHandleAndSeqVector ) ◆ BOOST_AUTO_TEST_CASE() [9/84] BOOST_AUTO_TEST_CASE ( BioseqHandleAndSeqVectorNonWriteDB ) ◆ BOOST_AUTO_TEST_CASE() [10/84] BOOST_AUTO_TEST_CASE ( BioseqHandleAndSeqVectorWriteDB ) ◆ BOOST_AUTO_TEST_CASE() [11/84] BOOST_AUTO_TEST_CASE ( CBuildDatabase_TestBasicDatabaseCreation )Definition at line 2661 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddIds(), CTmpFile::AsOutputFile(), CTmpFile::eIfExists_Reset, CBuildDatabase::EndBuild(), CWriteDB::eNoIndex, CFile::Exists(), kOutput, log, CRef< C, Locker >::Reset(), CBuildDatabase::SetSourceDb(), CBuildDatabase::SetTaxids(), CBuildDatabase::SetUseRemote(), and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [12/84] BOOST_AUTO_TEST_CASE ( CBuildDatabase_TestDirectoryCreation )Definition at line 2632 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddIds(), CTmpFile::AsOutputFile(), CTmpFile::eIfExists_Reset, CBuildDatabase::EndBuild(), CWriteDB::eNoIndex, CFile::Exists(), kOutput, log, CRef< C, Locker >::Reset(), CBuildDatabase::SetSourceDb(), CBuildDatabase::SetTaxids(), CBuildDatabase::SetUseRemote(), and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [13/84] BOOST_AUTO_TEST_CASE ( CBuildDatabase_TestQuickDatabaseCreation )Definition at line 2691 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CTmpFile::AsOutputFile(), CBuildDatabase::Build(), CTmpFile::eIfExists_Reset, CBuildDatabase::EndBuild(), CWriteDB::eNoIndex, CFile::Exists(), kOutput, log, CRef< C, Locker >::Reset(), and CBuildDatabase::SetSourceDb().
◆ BOOST_AUTO_TEST_CASE() [14/84] BOOST_AUTO_TEST_CASE ( CBuildDatabase_TestQuickDatabaseCreation_NoIds )Definition at line 2730 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CTmpFile::AsOutputFile(), CBuildDatabase::Build(), CTmpFile::eIfExists_Reset, CBuildDatabase::EndBuild(), CWriteDB::eNoIndex, CFile::Exists(), kOutput, log, CRef< C, Locker >::Reset(), and CBuildDatabase::SetSourceDb().
◆ BOOST_AUTO_TEST_CASE() [15/84] BOOST_AUTO_TEST_CASE ( CBuildDatabase_WGS_gap )Definition at line 2802 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddSequences(), CTmpFile::AsOutputFile(), CTmpFile::eIfExists_Reset, CBuildDatabase::EndBuild(), CWriteDB::eNoIndex, eSerial_AsnText, CFile::Exists(), kOutput, log, CObjectIStream::Open(), CRef< C, Locker >::Reset(), and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [16/84] BOOST_AUTO_TEST_CASE ( CBuildDatabase_WriteToInvalidPathUnix ) ◆ BOOST_AUTO_TEST_CASE() [17/84] BOOST_AUTO_TEST_CASE ( CBuildDatabase_WriteToInvalidPathWindows ) ◆ BOOST_AUTO_TEST_CASE() [18/84] BOOST_AUTO_TEST_CASE ( CreateV5Seqidlist )Definition at line 3262 of file writedb_unit_test.cpp.
References CTmpFile::AsOutputFile(), SBlastSeqIdListInfo::db_vol_length, CTmpFile::eIfExists_Reset, CSeqDB::eNucleotide, SBlastSeqIdListInfo::file_size, CTmpFile::GetFileName(), CMemoryFileMap::GetFileSize(), CBlastSeqidlistFile::GetSeqidlist(), CSeqDB::GetVolumeLength(), kTitle, NcbiGetlineEOL(), SBlastSeqIdListInfo::num_ids, out(), si, SBlastSeqIdListInfo::title, and WriteBlastSeqidlistFile().
◆ BOOST_AUTO_TEST_CASE() [19/84] BOOST_AUTO_TEST_CASE ( CWriteDB_SetTaxonomy )Definition at line 2525 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), CFastaReader::AtEOF(), CWriteDB::Close(), DeleteBlastDb(), CSeqDB::eNucleotide, CWriteDB::eNucleotide, CWriteDB::ExtractBioseqDeflines(), CFastaReader::fAssumeNuc, FindGi(), CTaxIdSet::FixTaxId(), flags, CBioseq_Base::GetId(), CSeqDB::GetNumSeqs(), CSeqDB::GetTaxIDs(), set< Key, Compare >::insert(), CSeq_entry_Base::IsSeq(), kTaxId, CRef< C, Locker >::NotEmpty(), CFastaReader::ReadOneSeq(), CWriteDB::SetDeflines(), CSeq_entry_Base::SetSeq(), and TAX_ID_CONST.
◆ BOOST_AUTO_TEST_CASE() [20/84] BOOST_AUTO_TEST_CASE ( CWriteDB_SetTaxonomyFromMap )Definition at line 2560 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), CFastaReader::AtEOF(), CWriteDB::Close(), DeleteBlastDb(), CSeqDB::eNucleotide, CWriteDB::eNucleotide, CWriteDB::ExtractBioseqDeflines(), CFastaReader::fAssumeNuc, FindGi(), CTaxIdSet::FixTaxId(), flags, CBioseq_Base::GetId(), CSeqDB::GetNumSeqs(), CSeqDB::GetTaxIDs(), set< Key, Compare >::insert(), CSeq_entry_Base::IsSeq(), kTaxId, CRef< C, Locker >::NotEmpty(), CFastaReader::ReadOneSeq(), CWriteDB::SetDeflines(), CTaxIdSet::SetMappingFromFile(), CSeq_entry_Base::SetSeq(), and TAX_ID_CONST.
◆ BOOST_AUTO_TEST_CASE() [21/84] BOOST_AUTO_TEST_CASE ( CWriteDB_SetTaxonomyFromMapLclIds )Definition at line 2597 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), CFastaReader::AtEOF(), CWriteDB::Close(), DeleteBlastDb(), CSeqDB::eNucleotide, CSeqDB::eProtein, CWriteDB::eProtein, CWriteDB::ExtractBioseqDeflines(), CFastaReader::fAssumeProt, CTaxIdSet::FixTaxId(), flags, CSeqDB::GetNumSeqs(), CSeqDB::GetTaxIDs(), CSeq_entry_Base::IsSeq(), kTaxId, CRef< C, Locker >::NotEmpty(), CFastaReader::ReadOneSeq(), CWriteDB::SetDeflines(), CTaxIdSet::SetMappingFromFile(), CSeq_entry_Base::SetSeq(), and TAX_ID_CONST.
◆ BOOST_AUTO_TEST_CASE() [22/84] BOOST_AUTO_TEST_CASE ( DuplicateAlgoId ) ◆ BOOST_AUTO_TEST_CASE() [23/84] BOOST_AUTO_TEST_CASE ( DuplicateId ) ◆ BOOST_AUTO_TEST_CASE() [24/84] BOOST_AUTO_TEST_CASE ( EmptyBioseq ) ◆ BOOST_AUTO_TEST_CASE() [25/84] BOOST_AUTO_TEST_CASE ( FastaReaderBioseq )Definition at line 1543 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), CWriteDB::Close(), CWriteDB::eFullIndex, CSeqDB::eProtein, CWriteDB::eProtein, CBlast_def_line_set_Base::Get(), CSeqDB::GetHdr(), CSeqDB::GetNumOIDs(), CWriteDB::ListFiles(), s_FastaStringToBioseq(), s_WrapUpFiles(), and str().
◆ BOOST_AUTO_TEST_CASE() [26/84] BOOST_AUTO_TEST_CASE ( FourAndEightByteTis )Definition at line 1634 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), CWriteDB::Close(), data4, CWriteDB::eFullWithTrace, CWriteDB::eNucleotide, SStaticPair< FirstType, SecondType >::first, i, NStr::Int8ToString(), ITERATE, s_FastaStringToBioseq(), s_HexDumpFile(), s_WrapUpDb(), SStaticPair< FirstType, SecondType >::second, and string.
◆ BOOST_AUTO_TEST_CASE() [27/84] BOOST_AUTO_TEST_CASE ( HashToOid )Definition at line 1433 of file writedb_unit_test.cpp.
References CWriteDB::Close(), CWriteDB::eAddHash, CWriteDB::eFullWithTrace, CSeqDB::eNucleotide, CWriteDB::eNucleotide, CSeqDB::eProtein, CWriteDB::eProtein, prot, s_BuildIds(), s_DupIdsBioseq(), and s_WrapUpDb().
◆ BOOST_AUTO_TEST_CASE() [28/84] BOOST_AUTO_TEST_CASE ( InvalidAliasFileGeneration_NoGisInBlastDB ) ◆ BOOST_AUTO_TEST_CASE() [29/84] BOOST_AUTO_TEST_CASE ( InvalidAliasFileGeneration_NonExistentDb ) ◆ BOOST_AUTO_TEST_CASE() [30/84] BOOST_AUTO_TEST_CASE ( InvalidAliasFileGeneration_NonExistentDbAggregation ) ◆ BOOST_AUTO_TEST_CASE() [31/84] BOOST_AUTO_TEST_CASE ( InvalidAliasFileGeneration_NonExistentMultiVolDbAggregation ) ◆ BOOST_AUTO_TEST_CASE() [32/84] BOOST_AUTO_TEST_CASE ( IsamSorting ) ◆ BOOST_AUTO_TEST_CASE() [33/84] BOOST_AUTO_TEST_CASE ( LimitProteinDeflines )Definition at line 3507 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CWriteDB::AddSequence(), CWriteDB::Close(), dbname(), eBDB_Version4, eDefault, CSeqDB::eProtein, CWriteDB::eProtein, CSeqDB::GetAllTaxIDs(), CSeqDB::GetHdr(), i, MSerial_AsnText, CBlast_def_line_set_Base::Set(), CWriteDB::SetDeflines(), and t.
◆ BOOST_AUTO_TEST_CASE() [34/84] BOOST_AUTO_TEST_CASE ( MaskDataBoundsError ) ◆ BOOST_AUTO_TEST_CASE() [35/84] BOOST_AUTO_TEST_CASE ( MaskDataColumn ) ◆ BOOST_AUTO_TEST_CASE() [36/84] BOOST_AUTO_TEST_CASE ( MismatchedDb_Bioseq ) ◆ BOOST_AUTO_TEST_CASE() [37/84] BOOST_AUTO_TEST_CASE ( MultiVolume )Definition at line 1263 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), CWriteDB::Close(), CWriteDB::eFullIndex, CSeqDB::eProtein, CWriteDB::eProtein, CSeqDB::eUnfilteredAll, f, CSeqDB::GetBioseq(), CSeqDB::GetSeqLength(), CSeqDB::GetTotals(), CSeqDB::GiToOid(), i, CWriteDB::ListFiles(), CWriteDB::ListVolumes(), CRef< C, Locker >::Reset(), s_WrapUpFiles(), and CWriteDB::SetMaxVolumeLetters().
◆ BOOST_AUTO_TEST_CASE() [38/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDup ) ◆ BOOST_AUTO_TEST_CASE() [39/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupI ) ◆ BOOST_AUTO_TEST_CASE() [40/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ ) ◆ BOOST_AUTO_TEST_CASE() [41/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ12 ) ◆ BOOST_AUTO_TEST_CASE() [42/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ16 ) ◆ BOOST_AUTO_TEST_CASE() [43/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ20 ) ◆ BOOST_AUTO_TEST_CASE() [44/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ24 ) ◆ BOOST_AUTO_TEST_CASE() [45/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ28 ) ◆ BOOST_AUTO_TEST_CASE() [46/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ32 ) ◆ BOOST_AUTO_TEST_CASE() [47/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ33 ) ◆ BOOST_AUTO_TEST_CASE() [48/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ34 ) ◆ BOOST_AUTO_TEST_CASE() [49/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ35 ) ◆ BOOST_AUTO_TEST_CASE() [50/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ36 ) ◆ BOOST_AUTO_TEST_CASE() [51/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ4 ) ◆ BOOST_AUTO_TEST_CASE() [52/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ40 ) ◆ BOOST_AUTO_TEST_CASE() [53/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ44 ) ◆ BOOST_AUTO_TEST_CASE() [54/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ45 ) ◆ BOOST_AUTO_TEST_CASE() [55/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ46 ) ◆ BOOST_AUTO_TEST_CASE() [56/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ47 ) ◆ BOOST_AUTO_TEST_CASE() [57/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ48 ) ◆ BOOST_AUTO_TEST_CASE() [58/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ49 ) ◆ BOOST_AUTO_TEST_CASE() [59/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ50 ) ◆ BOOST_AUTO_TEST_CASE() [60/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ8 ) ◆ BOOST_AUTO_TEST_CASE() [61/84] BOOST_AUTO_TEST_CASE ( NuclBioseqDupK ) ◆ BOOST_AUTO_TEST_CASE() [62/84] BOOST_AUTO_TEST_CASE ( PDBIdLowerCase )Definition at line 1500 of file writedb_unit_test.cpp.
References CSeqDB::AccessionToOids(), CWriteDB::AddSequence(), CWriteDB::Close(), CWriteDB::eFullIndex, CSeqDB::eProtein, CWriteDB::eProtein, CSeqDB::GetNumOIDs(), CWriteDB::ListFiles(), s_FastaStringToBioseq(), s_WrapUpFiles(), and str().
◆ BOOST_AUTO_TEST_CASE() [63/84] BOOST_AUTO_TEST_CASE ( ProtBioseqDup ) ◆ BOOST_AUTO_TEST_CASE() [64/84] BOOST_AUTO_TEST_CASE ( ReadBareIDNucleotide )Definition at line 3021 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddFasta(), CTmpFile::AsInputFile(), dbname(), CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Local, CSeq_id_Base::e_Other, CTmpFile::eIfExists_Throw, CBuildDatabase::EndBuild(), CSeqDB::eNucleotide, CTmpFile::GetFileName(), CSeqDB::GetSeqIDs(), NStr::IntToString(), log, and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [65/84] BOOST_AUTO_TEST_CASE ( ReadBareIDProtein )Definition at line 2891 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddFasta(), CTmpFile::AsInputFile(), dbname(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Local, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CTmpFile::eIfExists_Throw, CBuildDatabase::EndBuild(), CSeqDB::eProtein, CTmpFile::GetFileName(), CSeqDB::GetSeqIDs(), NStr::IntToString(), log, and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [66/84] BOOST_AUTO_TEST_CASE ( ReadMixIDNucleotide )Definition at line 3212 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddFasta(), CTmpFile::AsInputFile(), dbname(), CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Other, CTmpFile::eIfExists_Throw, CBuildDatabase::EndBuild(), CSeqDB::eNucleotide, CTmpFile::GetFileName(), CSeqDB::GetSeqIDs(), log, and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [67/84] BOOST_AUTO_TEST_CASE ( ReadMixIDsProtein )Definition at line 3081 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddFasta(), CTmpFile::AsInputFile(), dbname(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Local, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CTmpFile::eIfExists_Throw, CBuildDatabase::EndBuild(), CSeqDB::eProtein, CTmpFile::GetFileName(), CSeqDB::GetSeqIDs(), NStr::IntToString(), log, and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [68/84] BOOST_AUTO_TEST_CASE ( ReadMultipleBareIDs )Definition at line 2959 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddFasta(), CTmpFile::AsInputFile(), dbname(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Local, CSeq_id_Base::e_Other, CTmpFile::eIfExists_Throw, CBuildDatabase::EndBuild(), CSeqDB::eProtein, CTmpFile::GetFileName(), CSeqDB::GetSeqIDs(), NStr::IntToString(), log, and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [69/84] BOOST_AUTO_TEST_CASE ( ReadMultipleMixLongIDs )Definition at line 3150 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddFasta(), CTmpFile::AsInputFile(), dbname(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Local, CSeq_id_Base::e_Other, CTmpFile::eIfExists_Throw, CBuildDatabase::EndBuild(), CSeqDB::eProtein, CTmpFile::GetFileName(), CSeqDB::GetSeqIDs(), NStr::IntToString(), log, and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [70/84] BOOST_AUTO_TEST_CASE ( ReadMultiSeqIdsDefline )Definition at line 3338 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), CBuildDatabase::AddFasta(), dbname(), CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pdb, CBuildDatabase::EndBuild(), CSeqDB::eProtein, CSeqDB::GetSeqIDs(), log, and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [71/84] BOOST_AUTO_TEST_CASE ( ReadPDBAsn1 ) ◆ BOOST_AUTO_TEST_CASE() [72/84] BOOST_AUTO_TEST_CASE ( ReadPDBFasta )Definition at line 3382 of file writedb_unit_test.cpp.
References CSeqDB::AccessionsToOids(), CFileDeleteAtExit::Add(), CBuildDatabase::AddFasta(), CSeqDB::CheckOrFindOID(), dbname(), CSeq_id_Base::e_Pdb, eBDB_Version5, CBuildDatabase::EndBuild(), CSeqDB::eProtein, CSeqDB::GetSeqIDs(), CNcbiApplication::Instance(), ITERATE, kSeqDBEntryNotFound, log, CNcbiApplicationAPI::SetEnvironment(), and CBuildDatabase::StartBuild().
◆ BOOST_AUTO_TEST_CASE() [73/84] BOOST_AUTO_TEST_CASE ( RegisterMaskingAlgorithms ) ◆ BOOST_AUTO_TEST_CASE() [74/84] BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfDust ) ◆ BOOST_AUTO_TEST_CASE() [75/84] BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfOther ) ◆ BOOST_AUTO_TEST_CASE() [76/84] BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfRepeats ) ◆ BOOST_AUTO_TEST_CASE() [77/84] BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfSeg ) ◆ BOOST_AUTO_TEST_CASE() [78/84] BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfWindowMasker ) ◆ BOOST_AUTO_TEST_CASE() [79/84] BOOST_AUTO_TEST_CASE ( RegisterVariantsOfSameMaskingAlgorithm ) ◆ BOOST_AUTO_TEST_CASE() [80/84] BOOST_AUTO_TEST_CASE ( SetPig )Definition at line 1206 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), CSeqDB::CheckOrFindOID(), CWriteDB::Close(), CWriteDB::eFullIndex, CSeqDB::eProtein, CWriteDB::eProtein, CSeqDB::GetGis(), CSeqDB::GiToBioseq(), i, CWriteDB::ListFiles(), CSeqDB::OidToPig(), s_WrapUpFiles(), and CWriteDB::SetPig().
◆ BOOST_AUTO_TEST_CASE() [81/84] BOOST_AUTO_TEST_CASE ( TooManyAlgoId ) ◆ BOOST_AUTO_TEST_CASE() [82/84] BOOST_AUTO_TEST_CASE ( UndefinedAlgoID ) ◆ BOOST_AUTO_TEST_CASE() [83/84] BOOST_AUTO_TEST_CASE ( UserDefinedColumns ) ◆ BOOST_AUTO_TEST_CASE() [84/84] BOOST_AUTO_TEST_CASE ( UsPatId )Definition at line 1318 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), CWriteDB::Close(), CWriteDB::eFullIndex, CSeqDB::eProtein, CWriteDB::eProtein, CSeqDB::GiToBioseq(), CWriteDB::ListFiles(), s_WrapUpFiles(), CSeqDB::SeqidToOid(), CBlast_def_line_set_Base::Set(), and CWriteDB::SetDeflines().
◆ RegisterTooManyVariantsOfSameMaskingAlgorithm() void RegisterTooManyVariantsOfSameMaskingAlgorithm ( EBlast_filter_program masking_algo, size_t kMaxNumSupportedAlgorithmVariants ) ◆ s_AccToSeqId() ◆ s_BuildIds() [1/2] ◆ s_BuildIds() [2/2] ◆ s_CheckFiles() ◆ s_CheckSorted() ◆ s_CompareBioseqs() ◆ s_DupIdsBioseq()Definition at line 207 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), BOOST_REQUIRE_CUTPOINT, g_NuclJ_OidCount, CSeqDB::GetBioseq(), CSeq_id_Base::GetGi(), CSeqDB::GetHdr(), CSeq_id::GetSeqIdString(), CSeq_id_Base::IsGi(), ITERATE, CRef< C, Locker >::NotEmpty(), CSeqDB::SeqidToOid(), and CWriteDB::SetDeflines().
Referenced by BOOST_AUTO_TEST_CASE(), and s_DupSequencesTest().
◆ s_DupIdsRaw()Definition at line 269 of file writedb_unit_test.cpp.
References CWriteDB::AddSequence(), ambig(), CSeqDB::eNucleotide, CSeqDB::GetHdr(), CSeqDB::GetSequenceType(), ITERATE, CRef< C, Locker >::NotEmpty(), s_FetchRawData(), CSeqDB::SeqidToOid(), and CWriteDB::SetDeflines().
Referenced by s_DupSequencesTest().
◆ s_Duplicate()template<class ASNOBJ >
CRef<ASNOBJ> s_Duplicate ( const ASNOBJ & a ) ◆ s_DupSequencesTest()Definition at line 489 of file writedb_unit_test.cpp.
References CFileDeleteAtExit::Add(), basename, BOOST_REQUIRE_CUTPOINT, CWriteDB::Close(), CWriteDB::eFullIndex, CSeqDB::eNucleotide, CWriteDB::eNucleotide, CSeqDB::eProtein, CWriteDB::eProtein, i, CWriteDB::ListFiles(), CRef< C, Locker >::Reset(), s_DupIdsBioseq(), s_DupIdsRaw(), s_TestDatabase(), and CWrapperUpper::SetDb().
Referenced by BOOST_AUTO_TEST_CASE(), and s_NuclBioseqDupSwitch().
◆ s_ExtractLast() ◆ s_FastaStringToBioseq() ◆ s_FetchRawData() ◆ s_GetScope() ◆ s_GiToSeqId() ◆ s_HexDumpFile() [1/2] ◆ s_HexDumpFile() [2/2] ◆ s_HexDumpText() [1/2] ◆ s_HexDumpText() [2/2] ◆ s_NuclBioseqDupSwitch() static void s_NuclBioseqDupSwitch ( int cutpoint ) static ◆ s_RemoveFile() ◆ s_RemoveFiles() ◆ s_Stringify() ◆ s_TestDatabase() ◆ s_TestReadPDBAsn1()Definition at line 3435 of file writedb_unit_test.cpp.
References CSeqDB::AccessionsToOids(), CFileDeleteAtExit::Add(), CBuildDatabase::AddSequences(), CSeqDB::CheckOrFindOID(), dbname(), CSeq_id_Base::e_Pdb, eBDB_Version5, CBuildDatabase::EndBuild(), CSeqDB::eProtein, CSeqDB::GetSeqIDs(), i, CNcbiApplication::Instance(), ITERATE, log, MSerial_AsnText, CNcbiApplicationAPI::SetEnvironment(), and CBuildDatabase::StartBuild().
Referenced by BOOST_AUTO_TEST_CASE().
◆ s_Unstringify() ◆ s_WrapUpColumn() ◆ s_WrapUpDb() ◆ s_WrapUpFiles() ◆ USING_SCOPE() ◆ g_NuclJ_OidCount int g_NuclJ_OidCount = 99 ◆ USING_NCBI_SCOPERetroSearch is an open source project built by @garambo | Open a GitHub Issue
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