NCBI C++ ToolKit
Classes | Macros | Typedefs | Functions | Variables
writedb_unit_test.cpp File Reference
#include <ncbi_pch.hpp>
#include <objtools/blast/seqdb_reader/seqdbexpert.hpp>
#include <objtools/blast/seqdb_writer/writedb.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/seq_vector.hpp>
#include <objtools/readers/fasta.hpp>
#include <serial/objistr.hpp>
#include <serial/serial.hpp>
#include <serial/iterator.hpp>
#include "../mask_info_registry.hpp"
#include <sstream>
#include <corelib/test_boost.hpp>
#include <boost/current_function.hpp>
#include <objtools/blast/seqdb_writer/build_db.hpp>
#include <objtools/blast/seqdb_writer/writedb_isam.hpp>
#include <objtools/blast/seqdb_writer/seqidlist_writer.hpp>
#include <objtools/blast/seqdb_reader/impl/seqdbisam.hpp>
#include <objtools/blast/seqdb_reader/seqidlist_reader.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <unordered_map>
+ Include dependency graph for writedb_unit_test.cpp:

Go to the source code of this file.

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Classes

class  CNonException
 
class  CWrapperUpper
 
struct  SAliasFileData
 Auxiliary class to parse the contents of an alias file. More...
 
struct  SAliasFileData::Value
 Encapsulates the alias' file key-value pair. More...
 
class  CSeqEntryGetSource
 

Macros

#define NCBI_TEST_APPLICATION
 
#define BOOST_REQUIRE_CUTPOINT(X)   if (cutpoint == X) throw CNonException()
 

Typedefs

typedef vector< CRef< CSeq_id > > TIdList
 

Functions

 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)
 

Variables

 USING_NCBI_SCOPE
 
int g_NuclJ_OidCount = 99
 

Macro Definition Documentation

◆ BOOST_REQUIRE_CUTPOINT

#define BOOST_REQUIRE_CUTPOINT (   X)    if (cutpoint == X) throw CNonException()

Definition at line 202 of file writedb_unit_test.cpp.

◆ NCBI_TEST_APPLICATION

#define NCBI_TEST_APPLICATION

Definition at line 32 of file writedb_unit_test.cpp.

Typedef Documentation

◆ TIdList

typedef vector< CRef<CSeq_id> > TIdList

Definition at line 195 of file writedb_unit_test.cpp.

Function Documentation

◆ 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 2361 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 2326 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  )

Definition at line 1596 of file writedb_unit_test.cpp.

References CBinaryListBuilder::AppendId(), CBinaryListBuilder::eTi, i, CDirEntry::Remove(), s_HexDumpFile(), and CBinaryListBuilder::Write().

◆ BOOST_AUTO_TEST_CASE() [7/84]

BOOST_AUTO_TEST_CASE ( BioseqHandle  )

Definition at line 1113 of file writedb_unit_test.cpp.

References CWriteDB::AddSequence(), CWriteDB::Close(), CWriteDB::eFullIndex, CWriteDB::eProtein, CScope::GetBioseqHandle(), s_GetScope(), and s_WrapUpDb().

◆ BOOST_AUTO_TEST_CASE() [8/84]

BOOST_AUTO_TEST_CASE ( BioseqHandleAndSeqVector  )

Definition at line 1158 of file writedb_unit_test.cpp.

References CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeqVector::GetSeqData(), s_Duplicate(), s_GetScope(), and CSeqVector::size().

◆ BOOST_AUTO_TEST_CASE() [9/84]

BOOST_AUTO_TEST_CASE ( BioseqHandleAndSeqVectorNonWriteDB  )

Definition at line 1135 of file writedb_unit_test.cpp.

References CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeqVector::GetSeqData(), s_Duplicate(), s_GetScope(), and CSeqVector::size().

◆ BOOST_AUTO_TEST_CASE() [10/84]

BOOST_AUTO_TEST_CASE ( BioseqHandleAndSeqVectorWriteDB  )

Definition at line 1176 of file writedb_unit_test.cpp.

References CWriteDB::AddSequence(), CWriteDB::Close(), CWriteDB::eFullIndex, CWriteDB::eProtein, CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), s_Duplicate(), s_GetScope(), s_WrapUpDb(), and CBioseq_Base::SetInst().

◆ BOOST_AUTO_TEST_CASE() [11/84]

BOOST_AUTO_TEST_CASE ( CBuildDatabase_TestBasicDatabaseCreation  )

Definition at line 2665 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 2636 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 2695 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 2734 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 2806 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  )

Definition at line 2513 of file writedb_unit_test.cpp.

References CTmpFile::AsOutputFile(), CWriteDB::eDefault, CTmpFile::eIfExists_Reset, CRef< C, Locker >::Empty(), CFile::Exists(), kOutput, log, and CRef< C, Locker >::Reset().

◆ BOOST_AUTO_TEST_CASE() [17/84]

BOOST_AUTO_TEST_CASE ( CBuildDatabase_WriteToInvalidPathWindows  )

Definition at line 2495 of file writedb_unit_test.cpp.

References CTmpFile::AsOutputFile(), CWriteDB::eDefault, CTmpFile::eIfExists_Reset, CRef< C, Locker >::Empty(), kOutput, log, and CRef< C, Locker >::Reset().

◆ BOOST_AUTO_TEST_CASE() [18/84]

BOOST_AUTO_TEST_CASE ( CreateV5Seqidlist  )

Definition at line 3266 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 2529 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 2564 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 2601 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  )

Definition at line 2006 of file writedb_unit_test.cpp.

References eBlast_filter_program_seg, CWriteDB::eProtein, and W.

◆ BOOST_AUTO_TEST_CASE() [23/84]

BOOST_AUTO_TEST_CASE ( DuplicateId  )

Definition at line 1403 of file writedb_unit_test.cpp.

References s_BuildIds(), and s_DupSequencesTest().

◆ BOOST_AUTO_TEST_CASE() [24/84]

BOOST_AUTO_TEST_CASE ( EmptyBioseq  )

Definition at line 1099 of file writedb_unit_test.cpp.

References CWriteDB::AddSequence(), CWriteDB::Close(), CWriteDB::eFullIndex, and CWriteDB::eProtein.

◆ 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  )

Definition at line 2469 of file writedb_unit_test.cpp.

References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), CWriteDB::eProtein, CTmpFile::GetFileName(), and kTitle.

◆ BOOST_AUTO_TEST_CASE() [29/84]

BOOST_AUTO_TEST_CASE ( InvalidAliasFileGeneration_NonExistentDb  )

Definition at line 2397 of file writedb_unit_test.cpp.

References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), CWriteDB::eProtein, CTmpFile::GetFileName(), kTitle, and CDirEntry::Remove().

◆ BOOST_AUTO_TEST_CASE() [30/84]

BOOST_AUTO_TEST_CASE ( InvalidAliasFileGeneration_NonExistentDbAggregation  )

Definition at line 2419 of file writedb_unit_test.cpp.

References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), CWriteDB::eProtein, CTmpFile::GetFileName(), kEmptyStr, kTitle, and CDirEntry::Remove().

◆ BOOST_AUTO_TEST_CASE() [31/84]

BOOST_AUTO_TEST_CASE ( InvalidAliasFileGeneration_NonExistentMultiVolDbAggregation  )

Definition at line 2449 of file writedb_unit_test.cpp.

References CFileDeleteAtExit::Add(), CWriteDB_CreateAliasFile(), CWriteDB::eProtein, kTitle, and CDirEntry::Remove().

◆ BOOST_AUTO_TEST_CASE() [32/84]

BOOST_AUTO_TEST_CASE ( IsamSorting  )

Definition at line 1361 of file writedb_unit_test.cpp.

References s_BuildIds(), and s_DupSequencesTest().

◆ BOOST_AUTO_TEST_CASE() [33/84]

BOOST_AUTO_TEST_CASE ( LimitProteinDeflines  )

Definition at line 3511 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  )

Definition at line 2091 of file writedb_unit_test.cpp.

References eBlast_filter_program_dust, eBlast_filter_program_repeat, eBlast_filter_program_seg, CSeqDB::eProtein, CWriteDB::eProtein, int, s_WrapUpDb(), and W.

◆ BOOST_AUTO_TEST_CASE() [35/84]

BOOST_AUTO_TEST_CASE ( MaskDataColumn  )

Definition at line 1919 of file writedb_unit_test.cpp.

References eBlast_filter_program_repeat, eBlast_filter_program_seg, CSeqDB::eProtein, CWriteDB::eProtein, i, s_WrapUpDb(), and W.

◆ BOOST_AUTO_TEST_CASE() [36/84]

BOOST_AUTO_TEST_CASE ( MismatchedDb_Bioseq  )

Definition at line 1471 of file writedb_unit_test.cpp.

References CWriteDB::AddSequence(), CWriteDB::Close(), CWriteDB::eFullIndex, CWriteDB::eNucleotide, CWriteDB::ListFiles(), s_FastaStringToBioseq(), s_RemoveFiles(), and str().

◆ 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  )

Definition at line 1060 of file writedb_unit_test.cpp.

References s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [39/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupI  )

Definition at line 758 of file writedb_unit_test.cpp.

References s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [40/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ  )

Definition at line 1008 of file writedb_unit_test.cpp.

References s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [41/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ12  )

Definition at line 792 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [42/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ16  )

Definition at line 804 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [43/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ20  )

Definition at line 816 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [44/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ24  )

Definition at line 828 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [45/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ28  )

Definition at line 840 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [46/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ32  )

Definition at line 852 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [47/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ33  )

Definition at line 864 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [48/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ34  )

Definition at line 876 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [49/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ35  )

Definition at line 888 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [50/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ36  )

Definition at line 900 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [51/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ4  )

Definition at line 768 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [52/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ40  )

Definition at line 912 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [53/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ44  )

Definition at line 924 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [54/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ45  )

Definition at line 936 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [55/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ46  )

Definition at line 948 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [56/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ47  )

Definition at line 960 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [57/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ48  )

Definition at line 972 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [58/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ49  )

Definition at line 984 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [59/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ50  )

Definition at line 996 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [60/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupJ8  )

Definition at line 780 of file writedb_unit_test.cpp.

References g_NuclJ_OidCount, and s_NuclBioseqDupSwitch().

◆ BOOST_AUTO_TEST_CASE() [61/84]

BOOST_AUTO_TEST_CASE ( NuclBioseqDupK  )

Definition at line 1018 of file writedb_unit_test.cpp.

References s_NuclBioseqDupSwitch().

◆ 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  )

Definition at line 1066 of file writedb_unit_test.cpp.

References s_BuildIds(), and s_DupSequencesTest().

◆ BOOST_AUTO_TEST_CASE() [64/84]

BOOST_AUTO_TEST_CASE ( ReadBareIDNucleotide  )

Definition at line 3025 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 2895 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 3216 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 3085 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 2963 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 3154 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 3342 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  )

Definition at line 3495 of file writedb_unit_test.cpp.

References s_TestReadPDBAsn1().

◆ BOOST_AUTO_TEST_CASE() [72/84]

BOOST_AUTO_TEST_CASE ( ReadPDBFasta  )

Definition at line 3386 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  )

Definition at line 1807 of file writedb_unit_test.cpp.

References eBlast_filter_program_dust, eBlast_filter_program_other, eBlast_filter_program_repeat, eBlast_filter_program_seg, eBlast_filter_program_windowmasker, ITERATE, and registry.

◆ BOOST_AUTO_TEST_CASE() [74/84]

BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfDust  )

Definition at line 1884 of file writedb_unit_test.cpp.

References eBlast_filter_program_dust, eBlast_filter_program_seg, and RegisterTooManyVariantsOfSameMaskingAlgorithm().

◆ BOOST_AUTO_TEST_CASE() [75/84]

BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfOther  )

Definition at line 1912 of file writedb_unit_test.cpp.

References eBlast_filter_program_max, eBlast_filter_program_other, and RegisterTooManyVariantsOfSameMaskingAlgorithm().

◆ BOOST_AUTO_TEST_CASE() [76/84]

BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfRepeats  )

Definition at line 1905 of file writedb_unit_test.cpp.

References eBlast_filter_program_other, eBlast_filter_program_repeat, and RegisterTooManyVariantsOfSameMaskingAlgorithm().

◆ BOOST_AUTO_TEST_CASE() [77/84]

BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfSeg  )

Definition at line 1891 of file writedb_unit_test.cpp.

References eBlast_filter_program_seg, eBlast_filter_program_windowmasker, and RegisterTooManyVariantsOfSameMaskingAlgorithm().

◆ BOOST_AUTO_TEST_CASE() [78/84]

BOOST_AUTO_TEST_CASE ( RegisterTooManyVariantsOfWindowMasker  )

Definition at line 1898 of file writedb_unit_test.cpp.

References eBlast_filter_program_repeat, eBlast_filter_program_windowmasker, and RegisterTooManyVariantsOfSameMaskingAlgorithm().

◆ BOOST_AUTO_TEST_CASE() [79/84]

BOOST_AUTO_TEST_CASE ( RegisterVariantsOfSameMaskingAlgorithm  )

Definition at line 1826 of file writedb_unit_test.cpp.

References eBlast_filter_program_seg, and registry.

◆ 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  )

Definition at line 2019 of file writedb_unit_test.cpp.

References eBlast_filter_program_seg, eBlast_filter_program_windowmasker, CWriteDB::eProtein, i, NStr::SizetToString(), and W.

◆ BOOST_AUTO_TEST_CASE() [82/84]

BOOST_AUTO_TEST_CASE ( UndefinedAlgoID  )

Definition at line 2052 of file writedb_unit_test.cpp.

References eBlast_filter_program_dust, eBlast_filter_program_repeat, eBlast_filter_program_seg, CSeqDB::eProtein, CWriteDB::eProtein, int, s_WrapUpDb(), and W.

◆ BOOST_AUTO_TEST_CASE() [83/84]

BOOST_AUTO_TEST_CASE ( UserDefinedColumns  )

Definition at line 1737 of file writedb_unit_test.cpp.

References CBlastDbBlob::eNone, CSeqDB::eProtein, CWriteDB::eProtein, i, ITERATE, s_WrapUpColumn(), s_WrapUpDb(), W, and CBlastDbBlob::WriteString().

◆ 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 
)

Definition at line 1836 of file writedb_unit_test.cpp.

References eBlast_filter_program_repeat, i, registry, and NStr::SizetToString().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_AccToSeqId()

CRef<CSeq_id> s_AccToSeqId ( const char *  acc)

Definition at line 94 of file writedb_unit_test.cpp.

Referenced by s_BuildIds().

◆ s_BuildIds() [1/2]

static void s_BuildIds ( TIdList &  ids,
const char **  gis 
)
static

Definition at line 581 of file writedb_unit_test.cpp.

References s_AccToSeqId().

◆ s_BuildIds() [2/2]

static void s_BuildIds ( TIdList &  ids,
TGi *  gis 
)
static

Definition at line 574 of file writedb_unit_test.cpp.

References s_GiToSeqId(), and ZERO_GI.

Referenced by BOOST_AUTO_TEST_CASE(), and s_NuclBioseqDupSwitch().

◆ s_CheckFiles()

void s_CheckFiles ( const vector< string > &  files,
bool  need_hash = false 
)

Definition at line 423 of file writedb_unit_test.cpp.

References i, s_CheckSorted(), and s_ExtractLast().

Referenced by s_WrapUpFiles().

◆ s_CheckSorted()

void s_CheckSorted ( const string &  fname)

Definition at line 390 of file writedb_unit_test.cpp.

References file, and NcbiGetlineEOL().

Referenced by s_CheckFiles().

◆ s_CompareBioseqs()

void s_CompareBioseqs ( CBioseq &  src,
CBioseq &  dst 
)

Definition at line 333 of file writedb_unit_test.cpp.

References s_Stringify().

Referenced by s_TestDatabase().

◆ s_DupIdsBioseq()

static void s_DupIdsBioseq ( CWriteDB &  w,
CSeqDB &  s,
const TIdList &  ids,
int  cutpoint 
)
static

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()

static void s_DupIdsRaw ( CWriteDB &  w,
CSeqDBExpert &  seqdb,
const TIdList &  ids 
)
static

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)

Definition at line 320 of file writedb_unit_test.cpp.

References a, s_Stringify(), and s_Unstringify().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_DupSequencesTest()

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

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()

string s_ExtractLast ( const string &  data,
const string &  delim 
)

Definition at line 407 of file writedb_unit_test.cpp.

References data, and string.

Referenced by s_CheckFiles().

◆ s_FastaStringToBioseq()

CRef<CBioseq> s_FastaStringToBioseq ( const string &  str,
bool  protein 
)

Definition at line 588 of file writedb_unit_test.cpp.

References CRef< C, Locker >::Empty(), CFastaReader::fAssumeNuc, CFastaReader::fAssumeProt, flags, CSeq_entry_Base::IsSeq(), lr(), CFastaReader::ReadOneSeq(), CSeq_entry_Base::SetSeq(), and str().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_FetchRawData()

void s_FetchRawData ( CSeqDBExpert &  seqdb,
int  oid,
string &  sequence,
string &  ambig 
)

Definition at line 67 of file writedb_unit_test.cpp.

References ambig(), buffer, and CSeqDBExpert::GetRawSeqAndAmbig().

Referenced by s_DupIdsRaw().

◆ s_GetScope()

static CRef<CScope> s_GetScope ( )
static

Definition at line 552 of file writedb_unit_test.cpp.

References CScope::AddTopLevelSeqEntry(), eSerial_AsnText, CObjectManager::GetInstance(), CObjectIStream::Open(), and CRef< C, Locker >::Reset().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_GiToSeqId()

CRef<CSeq_id> s_GiToSeqId ( TGi  gi)

Definition at line 84 of file writedb_unit_test.cpp.

References CSeq_id_Base::e_Gi.

Referenced by s_BuildIds().

◆ s_HexDumpFile() [1/2]

string s_HexDumpFile ( const string &  fname,
const vector< int > &  layout,
int  base 
)

Definition at line 158 of file writedb_unit_test.cpp.

References buf, f, and s_HexDumpText().

Referenced by BOOST_AUTO_TEST_CASE(), and s_HexDumpFile().

◆ s_HexDumpFile() [2/2]

string s_HexDumpFile ( const string &  fname,
int  per,
int  base 
)

Definition at line 181 of file writedb_unit_test.cpp.

References s_HexDumpFile().

◆ s_HexDumpText() [1/2]

string s_HexDumpText ( const string &  raw,
const vector< int > &  layout,
int  base 
)

Definition at line 103 of file writedb_unit_test.cpp.

References i, int, mask, tmp, and NStr::UInt8ToString().

Referenced by s_HexDumpFile(), and s_HexDumpText().

◆ s_HexDumpText() [2/2]

string s_HexDumpText ( const string &  raw,
int  per,
int  base 
)

Definition at line 148 of file writedb_unit_test.cpp.

References s_HexDumpText().

◆ s_NuclBioseqDupSwitch()

static void s_NuclBioseqDupSwitch ( int  cutpoint)
static

Definition at line 616 of file writedb_unit_test.cpp.

References BOOST_REQUIRE_CUTPOINT, s_BuildIds(), and s_DupSequencesTest().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_RemoveFile()

void s_RemoveFile ( const string &  f)

Definition at line 373 of file writedb_unit_test.cpp.

References CDirEntry::eOnlyEmpty, f, and CDirEntry::Remove().

Referenced by s_RemoveFiles().

◆ s_RemoveFiles()

void s_RemoveFiles ( const vector< string > &  files)

Definition at line 381 of file writedb_unit_test.cpp.

References i, and s_RemoveFile().

Referenced by BOOST_AUTO_TEST_CASE(), and s_WrapUpFiles().

◆ s_Stringify()

template<class ASNOBJ >
void s_Stringify ( const ASNOBJ &  a,
string &  s 
)

Definition at line 300 of file writedb_unit_test.cpp.

References a, and MSerial_AsnText.

Referenced by s_CompareBioseqs(), and s_Duplicate().

◆ s_TestDatabase()

void s_TestDatabase ( CSeqDBExpert &  src,
const string &  name,
const string &  title 
)

Definition at line 346 of file writedb_unit_test.cpp.

References CSeqDB::CheckOrFindOID(), CSeqDB::GetBioseq(), CSeqDB::GetSequenceType(), CSeqDB::GetTitle(), CSeqDB::GiToOid(), CSeqDB::OidToGi(), s_CompareBioseqs(), and ZERO_GI.

Referenced by s_DupSequencesTest().

◆ s_TestReadPDBAsn1()

void s_TestReadPDBAsn1 ( CNcbiIfstream &  istr,
CNcbiIfstream &  ref_ids_file,
int  num_oids 
)

Definition at line 3439 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()

template<class ASNOBJ >
void s_Unstringify ( const string &  s,
ASNOBJ &  a 
)

Definition at line 310 of file writedb_unit_test.cpp.

References a, and MSerial_AsnText.

Referenced by s_Duplicate().

◆ s_WrapUpColumn()

void s_WrapUpColumn ( CWriteDB_ColumnBuilder &  cb)

Definition at line 1730 of file writedb_unit_test.cpp.

References CWriteDB_ColumnBuilder::ListFiles(), and s_WrapUpFiles().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_WrapUpDb()

void s_WrapUpDb ( CWriteDB &  db)

Definition at line 455 of file writedb_unit_test.cpp.

References CWriteDB::ListFiles(), and s_WrapUpFiles().

Referenced by BOOST_AUTO_TEST_CASE(), and CWrapperUpper::~CWrapperUpper().

◆ s_WrapUpFiles()

void s_WrapUpFiles ( const vector< string > &  files)

Definition at line 447 of file writedb_unit_test.cpp.

References s_CheckFiles(), and s_RemoveFiles().

Referenced by BOOST_AUTO_TEST_CASE(), s_WrapUpColumn(), and s_WrapUpDb().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ g_NuclJ_OidCount

int g_NuclJ_OidCount = 99

Definition at line 204 of file writedb_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), and s_DupIdsBioseq().

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 59 of file writedb_unit_test.cpp.

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