NCBI C++ ToolKit
Classes | Functions | Variables
blastinput_unit_test.cpp File Reference
#include <ncbi_pch.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Packed_seqint.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/NCBIeaa.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <corelib/ncbienv.hpp>
#include <objtools/readers/reader_exception.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <algo/blast/api/sseqloc.hpp>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/blastinput/blast_input.hpp>
#include <algo/blast/blastinput/blast_input_aux.hpp>
#include <algo/blast/blastinput/blast_fasta_input.hpp>
#include <algo/blast/blastinput/blast_asn1_input.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_vector.hpp>
#include <algo/blast/blastinput/blastp_args.hpp>
#include <algo/blast/blastinput/blastn_args.hpp>
#include <algo/blast/blastinput/blastx_args.hpp>
#include <algo/blast/blastinput/tblastn_args.hpp>
#include <algo/blast/blastinput/tblastx_args.hpp>
#include <algo/blast/blastinput/psiblast_args.hpp>
#include <algo/blast/blastinput/rpsblast_args.hpp>
#include "blast_input_unit_test_aux.hpp"
#include <unordered_map>
#include <corelib/test_boost.hpp>
+ Include dependency graph for blastinput_unit_test.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes

struct  SDubiousShortSequence
 

Functions

 USING_SCOPE (blast)
 
 USING_SCOPE (objects)
 
static CRef< CBlastInput > s_DeclareBlastInput (CNcbiIstream &input_file, const CBlastInputSourceConfig &iconfig, int batch_size=kMax_Int)
 
static CRef< CBlastInput > s_DeclareBlastInput (const string &user_input, const CBlastInputSourceConfig &iconfig)
 
 BOOST_AUTO_TEST_CASE (ReadAccession_MismatchNuclProt)
 
 BOOST_AUTO_TEST_CASE (ReadAccession_MismatchProtNucl)
 
 BOOST_AUTO_TEST_CASE (ReadGi_MismatchNuclProt)
 
 BOOST_AUTO_TEST_CASE (ReadGi_MismatchProtNucl)
 
 BOOST_AUTO_TEST_CASE (TestSmallDubiousSequences)
 
 BOOST_AUTO_TEST_CASE (ReadFastaWithDefline_MismatchProtNucl)
 
 BOOST_AUTO_TEST_CASE (ReadFastaWithDefline_MismatchNuclProt)
 
 BOOST_AUTO_TEST_CASE (ReadFastaWithDeflineProtein_Single)
 
 BOOST_AUTO_TEST_CASE (RawFastaWithSpaces)
 
 BOOST_AUTO_TEST_CASE (ReadProteinWithGaps)
 
 BOOST_AUTO_TEST_CASE (RawFastaNoSpaces)
 
 BOOST_AUTO_TEST_CASE (RawFastaNoSpaces_UpperCaseWithN_ReadDeltaSeq)
 
 BOOST_AUTO_TEST_CASE (ReadGenbankReport)
 
 BOOST_AUTO_TEST_CASE (ReadInvalidGi)
 
 BOOST_AUTO_TEST_CASE (ReadInvalidSeqId)
 
 BOOST_AUTO_TEST_CASE (ReadBadUserInput)
 
 BOOST_AUTO_TEST_CASE (ReadMultipleGis_WithBadInput)
 This unit test proves that if one input is bad, all of them are rejected. More...
 
 BOOST_AUTO_TEST_CASE (ReadEmptyUserInput)
 
 BOOST_AUTO_TEST_CASE (ReadSingleFasta_WithTitle)
 
static void s_ReadAndTestQueryFromString_CFastaReader (const string &input, TSeqPos expected_length)
 
 BOOST_AUTO_TEST_CASE (SingleSequenceString_CFastaReaderNoNewLineAfterSeq)
 
 BOOST_AUTO_TEST_CASE (SingleSequenceString_CFastaReaderWithNewLines)
 
 BOOST_AUTO_TEST_CASE (SingleSequenceString_CFastaReaderNoDeflineNoNewLines)
 
static void s_ReadAndTestQueryFromString (const string &input, TSeqPos expected_length, bool is_protein)
 
 BOOST_AUTO_TEST_CASE (SingleSequenceString_NoNewLineAfterSeq)
 
 BOOST_AUTO_TEST_CASE (SingleSequenceString_WithNewLines)
 
 BOOST_AUTO_TEST_CASE (SingleSequenceString_NoDeflineNoNewLines)
 
 BOOST_AUTO_TEST_CASE (ReadEmptyUserInput_OnlyTitle)
 
 BOOST_AUTO_TEST_CASE (ReadSingleAccession)
 
 BOOST_AUTO_TEST_CASE (ReadSingleAccession_RetrieveLargeSequence)
 
 BOOST_AUTO_TEST_CASE_TIMEOUT (ReadSingleAccession_RetrieveLargeSequence, kTimeOutLargeSeq)
 
 BOOST_AUTO_TEST_CASE (ReadSingleAccession_RetrieveLargeSequenceWithRange)
 
 BOOST_AUTO_TEST_CASE_TIMEOUT (ReadSingleAccession_RetrieveLargeSequenceWithRange, kTimeOutLargeSeqWithRange)
 
 BOOST_AUTO_TEST_CASE (ReadMultipleAccessions)
 
 BOOST_AUTO_TEST_CASE (ReadMultipleAccessionsFromMemory)
 
 BOOST_AUTO_TEST_CASE (ReadSingleGi)
 
 BOOST_AUTO_TEST_CASE (ReadMultipleGis)
 
 BOOST_AUTO_TEST_CASE (ReadMultipleSequencesFromSequencer)
 
 BOOST_AUTO_TEST_CASE (ReadMultipleSequencesFromSequencerParseLocalIds)
 
 BOOST_AUTO_TEST_CASE (ReadSequenceWithlclID)
 
 BOOST_AUTO_TEST_CASE (ReadMultipleSequences_OneEmpty)
 
 BOOST_AUTO_TEST_CASE (ReadMultipleTis)
 
 BOOST_AUTO_TEST_CASE (ReadSingleTi)
 
 BOOST_AUTO_TEST_CASE (ReadAccessionsAndGisWithNewLines)
 
static string * s_FileContents2String (const char *file_name)
 
 BOOST_AUTO_TEST_CASE (ReadAccessionNucleotideIntoBuffer_Single)
 
 BOOST_AUTO_TEST_CASE (ReadGiNuclWithFlankingSpacesIntoBuffer_Single)
 
 BOOST_AUTO_TEST_CASE (ReadAccessionNuclWithFlankingSpacesIntoBuffer_Single)
 
 BOOST_AUTO_TEST_CASE (ReadFastaWithDeflineProteinIntoBuffer_Single)
 
 BOOST_AUTO_TEST_CASE (RangeBoth)
 
 BOOST_AUTO_TEST_CASE (RangeStartOnly)
 
 BOOST_AUTO_TEST_CASE (RangeInvalid_FromGreaterThanTo)
 
 BOOST_AUTO_TEST_CASE (RangeInvalid_FromGreaterThanSequenceLength)
 
 BOOST_AUTO_TEST_CASE (RangeInvalid_ToEqualThanSequenceLength)
 
 BOOST_AUTO_TEST_CASE (RangeInvalid_ToGreaterThanSequenceLength)
 
 BOOST_AUTO_TEST_CASE (ParseDefline)
 
 BOOST_AUTO_TEST_CASE (BadProtStrand)
 
 BOOST_AUTO_TEST_CASE (ReadFastaWithDeflineNucl_Multiple)
 
 BOOST_AUTO_TEST_CASE (NuclStrand)
 
 BOOST_AUTO_TEST_CASE (NuclLcaseMask_TSeqLocVector)
 
 BOOST_AUTO_TEST_CASE (NuclLcaseMask_BlastQueryVector)
 
 BOOST_AUTO_TEST_CASE (MultiSeq)
 
 BOOST_AUTO_TEST_CASE (MultiRange)
 
 BOOST_AUTO_TEST_CASE (MultiBatch)
 
 BOOST_AUTO_TEST_CASE (NoDeflineExpected)
 
 BOOST_AUTO_TEST_CASE (NoDeflineUnexpected)
 
 BOOST_AUTO_TEST_CASE (wb325_1)
 
 BOOST_AUTO_TEST_CASE (wb325_2)
 
 BOOST_AUTO_TEST_CASE (wb325_single1)
 
 BOOST_AUTO_TEST_CASE (wb325_single2)
 
 BOOST_AUTO_TEST_CASE (ReadSinglePdb)
 
 BOOST_AUTO_TEST_CASE (ThrowOnEmptySequence)
 
 BOOST_AUTO_TEST_CASE (FetchSraID)
 
 BOOST_AUTO_TEST_CASE (ReadSinglePdb_InDifferentFormats)
 
 BOOST_AUTO_TEST_CASE (RawFastaNoSpaces_UpperCaseWithN)
 
template<typename T >
void s_Ignore (const T &)
 
 BOOST_AUTO_TEST_CASE (ParseSequenceRange_EmptyRange)
 
 BOOST_AUTO_TEST_CASE (ParseSequenceRange_0BasedRange)
 
 BOOST_AUTO_TEST_CASE (ParseSequenceRange_InvalidDelimiter)
 
 BOOST_AUTO_TEST_CASE (ParseSequenceRange_IncompleteRange)
 
 BOOST_AUTO_TEST_CASE (ParseSequenceRange_InvalidRange)
 
 BOOST_AUTO_TEST_CASE (ParseSequenceRange_1BasedRange)
 
 BOOST_AUTO_TEST_CASE (CheckQueryBatchSize)
 
 BOOST_AUTO_TEST_CASE (FetchGiFromAccessionInput)
 
 BOOST_AUTO_TEST_SUITE_END () static int s_GetSegmentFlags(const CBioseq &bioseq)
 
static string s_GetSequenceId (const CBioseq &bioseq)
 
 BOOST_AUTO_TEST_CASE (TestPairedReadsFromFasta)
 
 BOOST_AUTO_TEST_CASE (TestPairedReadsFromTwoFastaFiles)
 
 BOOST_AUTO_TEST_CASE (TestSingleReadsFromFasta)
 
 BOOST_AUTO_TEST_CASE (TestPairedReadsFromFastQ)
 
 BOOST_AUTO_TEST_CASE (TestPairedReadsFromTwoFastQFiles)
 
 BOOST_AUTO_TEST_CASE (TestPairedReadsFromASN1)
 
 BOOST_AUTO_TEST_CASE (TestPairedReadsFromTwoASN1Files)
 
 BOOST_AUTO_TEST_CASE (TestPairedReadsFromFastC)
 
 BOOST_AUTO_TEST_SUITE_END () class CString2Args
 Auxiliary class to convert a string into an argument count and vector. More...
 
 BOOST_AUTO_TEST_CASE (PsiBlastAppTestMatrix)
 
 BOOST_AUTO_TEST_CASE (RpsBlastCBS)
 
 BOOST_AUTO_TEST_CASE (CheckMutuallyExclusiveOptions)
 
 BOOST_AUTO_TEST_CASE (CheckDiscoMegablast)
 
 BOOST_AUTO_TEST_CASE (CheckPercentIdentity)
 
 BOOST_AUTO_TEST_CASE (CheckNoGreedyExtension)
 
 BOOST_AUTO_TEST_CASE (CheckCulling)
 
 BOOST_AUTO_TEST_CASE (CheckTaskArgs)
 
 BOOST_AUTO_TEST_CASE (CheckQueryCoveragePercent)
 
 BOOST_AUTO_TEST_CASE (CheckMaxHspsPerSubject)
 

Variables

 USING_NCBI_SCOPE
 
const int kTimeOutLargeSeq = 60
 
const int kTimeOutLargeSeqWithRange = 60
 

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/96]

BOOST_AUTO_TEST_CASE ( BadProtStrand  )

Definition at line 2095 of file blastinput_unit_test.cpp.

References CInputException::eInvalidStrand, eNa_strand_both, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetStrand(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [2/96]

BOOST_AUTO_TEST_CASE ( CheckCulling  )

Definition at line 3376 of file blastinput_unit_test.cpp.

References NON_CONST_ITERATE.

◆ BOOST_AUTO_TEST_CASE() [3/96]

BOOST_AUTO_TEST_CASE ( CheckDiscoMegablast  )

Definition at line 3326 of file blastinput_unit_test.cpp.

References CBlastAppArgs::SetOptions().

◆ BOOST_AUTO_TEST_CASE() [4/96]

BOOST_AUTO_TEST_CASE ( CheckMaxHspsPerSubject  )

Definition at line 3429 of file blastinput_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [5/96]

BOOST_AUTO_TEST_CASE ( CheckMutuallyExclusiveOptions  )

Definition at line 3306 of file blastinput_unit_test.cpp.

References NON_CONST_ITERATE.

◆ BOOST_AUTO_TEST_CASE() [6/96]

BOOST_AUTO_TEST_CASE ( CheckNoGreedyExtension  )

Definition at line 3364 of file blastinput_unit_test.cpp.

References CBlastAppArgs::SetOptions().

◆ BOOST_AUTO_TEST_CASE() [7/96]

BOOST_AUTO_TEST_CASE ( CheckPercentIdentity  )

Definition at line 3350 of file blastinput_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [8/96]

BOOST_AUTO_TEST_CASE ( CheckQueryBatchSize  )

Definition at line 2808 of file blastinput_unit_test.cpp.

References eBlastn, and GetQueryBatchSize().

◆ BOOST_AUTO_TEST_CASE() [9/96]

BOOST_AUTO_TEST_CASE ( CheckQueryCoveragePercent  )

Definition at line 3415 of file blastinput_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [10/96]

BOOST_AUTO_TEST_CASE ( CheckTaskArgs  )

Definition at line 3400 of file blastinput_unit_test.cpp.

References CBlastOptionsFactory::eNuclNucl, CBlastOptionsFactory::eProtProt, CBlastOptionsFactory::GetTasks(), and CRef< C, Locker >::Reset().

◆ BOOST_AUTO_TEST_CASE() [11/96]

BOOST_AUTO_TEST_CASE ( FetchGiFromAccessionInput  )

Definition at line 2814 of file blastinput_unit_test.cpp.

References SDataLoaderConfig::eUseBlastDbDataLoader, SDataLoaderConfig::eUseGenbankDataLoader, CBlastInput::GetAllSeqLocs(), CScope::GetObjectManager(), input(), ITERATE, CBlastScopeSource::NewScope(), CSeq_id::PreferAccessionOverGi(), and CObjectManager::RevokeAllDataLoaders().

◆ BOOST_AUTO_TEST_CASE() [12/96]

BOOST_AUTO_TEST_CASE ( FetchSraID  )

Definition at line 2585 of file blastinput_unit_test.cpp.

References CBioseq_Handle::eCoding_Iupac, CDbtag::eDbtagType_SRA, SDataLoaderConfig::eUseGenbankDataLoader, CAliasBase< TPrim >::Get(), CScope::GetBioseqHandle(), CBioseq_Base::GetInst(), CObjectManager::GetInstance(), CSeq_data_Base::GetIupacna(), CSeq_inst_Base::GetLength(), CScope::GetObjectManager(), CSeq_inst_Base::GetSeq_data(), CBioseq_set_Base::GetSeq_set(), CBioseq_Handle::GetSeqVector(), i, infile, CSeq_data_Base::IsIupacna(), CSeq_inst_Base::IsSetSeq_data(), min(), msg(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CSeqVector::size(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [13/96]

BOOST_AUTO_TEST_CASE ( MultiBatch  )

Definition at line 2325 of file blastinput_unit_test.cpp.

References CSeq_id_Base::e_Gi, CSeq_id_Base::e_Swissprot, CObjectManager::GetInstance(), CScope::GetObjectManager(), GI_CONST, infile, IsLocalId(), CSeq_id::PreferAccessionOverGi(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetBelieveDeflines(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [14/96]

BOOST_AUTO_TEST_CASE ( MultiRange  )

Definition at line 2304 of file blastinput_unit_test.cpp.

References eExtreme_Positional, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, NON_CONST_ITERATE, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRange(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [15/96]

BOOST_AUTO_TEST_CASE ( MultiSeq  )

Definition at line 2290 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [16/96]

BOOST_AUTO_TEST_CASE ( NoDeflineExpected  )

Definition at line 2416 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [17/96]

BOOST_AUTO_TEST_CASE ( NoDeflineUnexpected  )

Definition at line 2430 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetBelieveDeflines(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [18/96]

BOOST_AUTO_TEST_CASE ( NuclLcaseMask_BlastQueryVector  )

Definition at line 2238 of file blastinput_unit_test.cpp.

References CRef< C, Locker >::Empty(), eNa_strand_minus, eNa_strand_plus, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, query, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetLowercaseMask(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [19/96]

BOOST_AUTO_TEST_CASE ( NuclLcaseMask_TSeqLocVector  )

Definition at line 2200 of file blastinput_unit_test.cpp.

References eNa_strand_both, eNa_strand_plus, CBlastInputSourceConfig::GetBelieveDeflines(), CObjectManager::GetInstance(), CBlastInputSourceConfig::GetLowercaseMask(), CScope::GetObjectManager(), CBlastInputSourceConfig::GetStrand(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetLowercaseMask(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [20/96]

BOOST_AUTO_TEST_CASE ( NuclStrand  )

Definition at line 2159 of file blastinput_unit_test.cpp.

References eNa_strand_minus, eNa_strand_plus, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), ITERATE, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetStrand(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [21/96]

BOOST_AUTO_TEST_CASE ( ParseDefline  )

Definition at line 2060 of file blastinput_unit_test.cpp.

References CSeq_id_Base::e_Gi, CSeq_id_Base::e_Swissprot, CObjectManager::GetInstance(), CScope::GetObjectManager(), GI_CONST, infile, IsLocalId(), CSeq_id::PreferAccessionOverGi(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetBelieveDeflines(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [22/96]

BOOST_AUTO_TEST_CASE ( ParseSequenceRange_0BasedRange  )

Definition at line 2766 of file blastinput_unit_test.cpp.

References ParseSequenceRange(), r(), and s_Ignore().

◆ BOOST_AUTO_TEST_CASE() [23/96]

BOOST_AUTO_TEST_CASE ( ParseSequenceRange_1BasedRange  )

Definition at line 2801 of file blastinput_unit_test.cpp.

References ParseSequenceRange(), r(), and U.

◆ BOOST_AUTO_TEST_CASE() [24/96]

BOOST_AUTO_TEST_CASE ( ParseSequenceRange_EmptyRange  )

Definition at line 2759 of file blastinput_unit_test.cpp.

References ParseSequenceRange(), r(), and s_Ignore().

◆ BOOST_AUTO_TEST_CASE() [25/96]

BOOST_AUTO_TEST_CASE ( ParseSequenceRange_IncompleteRange  )

Definition at line 2780 of file blastinput_unit_test.cpp.

References ParseSequenceRange(), r(), and s_Ignore().

◆ BOOST_AUTO_TEST_CASE() [26/96]

BOOST_AUTO_TEST_CASE ( ParseSequenceRange_InvalidDelimiter  )

Definition at line 2773 of file blastinput_unit_test.cpp.

References ParseSequenceRange(), r(), and s_Ignore().

◆ BOOST_AUTO_TEST_CASE() [27/96]

BOOST_AUTO_TEST_CASE ( ParseSequenceRange_InvalidRange  )

Definition at line 2791 of file blastinput_unit_test.cpp.

References ParseSequenceRange(), and r().

◆ BOOST_AUTO_TEST_CASE() [28/96]

BOOST_AUTO_TEST_CASE ( PsiBlastAppTestMatrix  )

Definition at line 3285 of file blastinput_unit_test.cpp.

References CBlastOptions::GetMatrixName(), CBlastOptionsHandle::GetOptions(), and CBlastAppArgs::SetOptions().

◆ BOOST_AUTO_TEST_CASE() [29/96]

BOOST_AUTO_TEST_CASE ( RangeBoth  )

Definition at line 1926 of file blastinput_unit_test.cpp.

References eExtreme_Positional, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRange(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [30/96]

BOOST_AUTO_TEST_CASE ( RangeInvalid_FromGreaterThanSequenceLength  )

Definition at line 1988 of file blastinput_unit_test.cpp.

References CInputException::eInvalidRange, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRange(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [31/96]

BOOST_AUTO_TEST_CASE ( RangeInvalid_FromGreaterThanTo  )

Definition at line 1967 of file blastinput_unit_test.cpp.

References CInputException::eInvalidRange, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRange(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [32/96]

BOOST_AUTO_TEST_CASE ( RangeInvalid_ToEqualThanSequenceLength  )

Definition at line 2008 of file blastinput_unit_test.cpp.

References eNa_strand_unknown, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRange(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [33/96]

BOOST_AUTO_TEST_CASE ( RangeInvalid_ToGreaterThanSequenceLength  )

Definition at line 2034 of file blastinput_unit_test.cpp.

References eNa_strand_unknown, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRange(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [34/96]

BOOST_AUTO_TEST_CASE ( RangeStartOnly  )

Definition at line 1947 of file blastinput_unit_test.cpp.

References eExtreme_Positional, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRange(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [35/96]

BOOST_AUTO_TEST_CASE ( RawFastaNoSpaces  )

Definition at line 463 of file blastinput_unit_test.cpp.

References CSeq_id_Base::e_Local, eNa_strand_both, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), CRef< C, Locker >::NotEmpty(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [36/96]

BOOST_AUTO_TEST_CASE ( RawFastaNoSpaces_UpperCaseWithN  )

Definition at line 2713 of file blastinput_unit_test.cpp.

References CBioseq_set_Base::CanGetSeq_set(), CSeq_id_Base::e_Local, eNa_strand_both, CSeq_inst_Base::eRepr_raw, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), infile, IsLocalId(), kEmptyStr, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CNcbiEnvironment::Set(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [37/96]

BOOST_AUTO_TEST_CASE ( RawFastaNoSpaces_UpperCaseWithN_ReadDeltaSeq  )

Definition at line 499 of file blastinput_unit_test.cpp.

References CBioseq_set_Base::CanGetSeq_set(), env, CSeq_inst_Base::eRepr_delta, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [38/96]

BOOST_AUTO_TEST_CASE ( RawFastaWithSpaces  )

Definition at line 386 of file blastinput_unit_test.cpp.

References CSeq_id_Base::e_Local, eNa_strand_both, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [39/96]

BOOST_AUTO_TEST_CASE ( ReadAccession_MismatchNuclProt  )

Definition at line 98 of file blastinput_unit_test.cpp.

References CInputException::eSequenceMismatch, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [40/96]

BOOST_AUTO_TEST_CASE ( ReadAccession_MismatchProtNucl  )

Definition at line 125 of file blastinput_unit_test.cpp.

References CInputException::eSequenceMismatch, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [41/96]

BOOST_AUTO_TEST_CASE ( ReadAccessionNucleotideIntoBuffer_Single  )

Definition at line 1678 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Other, eNa_strand_both, CSeq_inst_Base::eRepr_raw, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), IsLocalId(), CSeq_inst::IsNa(), om, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), s_FileContents2String(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [42/96]

BOOST_AUTO_TEST_CASE ( ReadAccessionNuclWithFlankingSpacesIntoBuffer_Single  )

Definition at line 1806 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Gi, eNa_strand_both, CSeq_inst_Base::eRepr_raw, NStr::Find(), CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), GI_CONST, IsLocalId(), CSeq_inst::IsNa(), ITERATE, NPOS, om, CSeq_id::PreferAccessionOverGi(), CObjectManager::RevokeAllDataLoaders(), rapidjson::source, TSeqLocVector2Bioseqs(), and dtl::version.

◆ BOOST_AUTO_TEST_CASE() [43/96]

BOOST_AUTO_TEST_CASE ( ReadAccessionsAndGisWithNewLines  )

Definition at line 1577 of file blastinput_unit_test.cpp.

References abort(), CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Other, eNa_strand_both, NStr::fConvErr_NoThrow, GetId(), CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), i, infile, IsLocalId(), SDataLoaderConfig::m_BlastDbName, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetDataLoaderConfig(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, TSeqLocVector2Bioseqs(), dtl::version, and ZERO_GI.

◆ BOOST_AUTO_TEST_CASE() [44/96]

BOOST_AUTO_TEST_CASE ( ReadBadUserInput  )

Definition at line 617 of file blastinput_unit_test.cpp.

References CRef< C, Locker >::Empty(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [45/96]

BOOST_AUTO_TEST_CASE ( ReadEmptyUserInput  )

Definition at line 679 of file blastinput_unit_test.cpp.

References CInputException::eEmptyUserInput, ctll::empty(), CRef< C, Locker >::Empty(), CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), NPOS, om, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, TSeqLocVector2Bioseqs(), and CException::what().

◆ BOOST_AUTO_TEST_CASE() [46/96]

BOOST_AUTO_TEST_CASE ( ReadEmptyUserInput_OnlyTitle  )

Definition at line 851 of file blastinput_unit_test.cpp.

References CheckForEmptySequences(), CInputException::eEmptyUserInput, ctll::empty(), CRef< C, Locker >::Empty(), CException::GetErrCode(), CTmpFile::GetFileName(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), NPOS, om, out(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, TSeqLocVector2Bioseqs(), and CException::what().

◆ BOOST_AUTO_TEST_CASE() [47/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDefline_MismatchNuclProt  )

Definition at line 331 of file blastinput_unit_test.cpp.

References CInputException::eSequenceMismatch, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetSeqLenThreshold2Guess(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [48/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDefline_MismatchProtNucl  )

Definition at line 308 of file blastinput_unit_test.cpp.

References CInputException::eSequenceMismatch, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetSeqLenThreshold2Guess(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [49/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDeflineNucl_Multiple  )

Definition at line 2118 of file blastinput_unit_test.cpp.

References eExtreme_Positional, eNa_strand_both, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetStrand(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [50/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDeflineProtein_Single  )

Definition at line 354 of file blastinput_unit_test.cpp.

References CSeq_id_Base::e_Local, eNa_strand_unknown, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [51/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDeflineProteinIntoBuffer_Single  )

Definition at line 1879 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Local, CSeq_inst_Base::eMol_aa, eNa_strand_unknown, CSeq_inst_Base::eRepr_raw, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), IsLocalId(), om, CObjectManager::RevokeAllDataLoaders(), s_FileContents2String(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [52/96]

BOOST_AUTO_TEST_CASE ( ReadGenbankReport  )

Definition at line 525 of file blastinput_unit_test.cpp.

References CSeq_id_Base::e_Local, eDiag_Warning, eNa_strand_both, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), SetDiagPostLevel(), SetDiagStream(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [53/96]

BOOST_AUTO_TEST_CASE ( ReadGi_MismatchNuclProt  )

Definition at line 152 of file blastinput_unit_test.cpp.

References CInputException::eSequenceMismatch, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [54/96]

BOOST_AUTO_TEST_CASE ( ReadGi_MismatchProtNucl  )

Definition at line 179 of file blastinput_unit_test.cpp.

References CInputException::eSequenceMismatch, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [55/96]

BOOST_AUTO_TEST_CASE ( ReadGiNuclWithFlankingSpacesIntoBuffer_Single  )

Definition at line 1732 of file blastinput_unit_test.cpp.

References b, CSeq_id::BestRank(), CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gi, eNa_strand_both, CSeq_inst_Base::eRepr_raw, FindBestChoice(), CTextseq_id_Base::GetAccession(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGi(), CObjectManager::GetInstance(), CTextseq_id_Base::GetName(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), CTextseq_id_Base::GetVersion(), GI_CONST, IsLocalId(), CSeq_inst::IsNa(), NotNull(), om, CSeq_id::PreferAccessionOverGi(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, TSeqLocVector2Bioseqs(), and CSeq_id_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [56/96]

BOOST_AUTO_TEST_CASE ( ReadInvalidGi  )

Definition at line 568 of file blastinput_unit_test.cpp.

References CInputException::eSeqIdNotFound, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [57/96]

BOOST_AUTO_TEST_CASE ( ReadInvalidSeqId  )

Definition at line 593 of file blastinput_unit_test.cpp.

References CSeqIdException::eFormat, CException::GetErrCode(), CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, msg(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [58/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleAccessions  )

Definition at line 1139 of file blastinput_unit_test.cpp.

References abort(), CSeq_id_Base::e_Other, eNa_strand_both, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), i, infile, IsLocalId(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, TSeqLocVector2Bioseqs(), and dtl::version.

◆ BOOST_AUTO_TEST_CASE() [59/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleAccessionsFromMemory  )

Definition at line 1202 of file blastinput_unit_test.cpp.

References eNa_strand_unknown, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), i, IsLocalId(), ITERATE, msg(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [60/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleGis  )

Definition at line 1311 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Gi, eNa_strand_both, CSeq_inst_Base::eRepr_raw, first(), CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), GI_FROM, i, infile, IsLocalId(), CSeq_inst::IsNa(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [61/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleGis_WithBadInput  )

This unit test proves that if one input is bad, all of them are rejected.

Definition at line 654 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [62/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleSequences_OneEmpty  )

Definition at line 1434 of file blastinput_unit_test.cpp.

References CheckForEmptySequences(), CObjectManager::GetInstance(), GetLength(), CScope::GetObjectManager(), i, infile, IsLocalId(), ITERATE, NPOS, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [63/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleSequencesFromSequencer  )

Definition at line 1375 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [64/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleSequencesFromSequencerParseLocalIds  )

Definition at line 1392 of file blastinput_unit_test.cpp.

References eNa_strand_other, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), NMacroArgs::kIsProtein, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [65/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleTis  )

Definition at line 1471 of file blastinput_unit_test.cpp.

References CSeq_id_Base::e_General, eNa_strand_both, first(), CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CObject_id_Base::GetId(), CSeq_interval_Base::GetId(), CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), CDbtag_Base::GetTag(), CSeq_interval_Base::GetTo(), i, infile, IsLocalId(), CSeq_interval_Base::IsSetId(), SDataLoaderConfig::m_BlastDbName, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetDataLoaderConfig(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, TSeqLocVector2Bioseqs(), and CSeq_id_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [66/96]

BOOST_AUTO_TEST_CASE ( ReadProteinWithGaps  )

Definition at line 419 of file blastinput_unit_test.cpp.

References CBioseq_Handle::eCoding_Iupac, CAliasBase< TPrim >::Get(), CScope::GetBioseqHandle(), CBioseq_Base::GetInst(), CObjectManager::GetInstance(), CSeq_inst_Base::GetLength(), CSeq_data_Base::GetNcbieaa(), CScope::GetObjectManager(), CSeq_inst_Base::GetSeq_data(), CBioseq_set_Base::GetSeq_set(), CBioseq_Handle::GetSeqVector(), i, infile, IsLocalId(), CSeq_data_Base::IsNcbieaa(), CSeq_inst_Base::IsSetSeq_data(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CSeqVector::size(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [67/96]

BOOST_AUTO_TEST_CASE ( ReadSequenceWithlclID  )

Definition at line 1415 of file blastinput_unit_test.cpp.

References eNa_strand_other, CObjectManager::GetInstance(), CScope::GetObjectManager(), infile, IsLocalId(), NMacroArgs::kIsProtein, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [68/96]

BOOST_AUTO_TEST_CASE ( ReadSingleAccession  )

Definition at line 945 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Other, eNa_strand_both, CSeq_inst_Base::eRepr_raw, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), infile, IsLocalId(), CSeq_inst::IsNa(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [69/96]

BOOST_AUTO_TEST_CASE ( ReadSingleAccession_RetrieveLargeSequence  )

Definition at line 994 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Other, eNa_strand_both, CSeq_inst_Base::eRepr_delta, NStr::Find(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), GI_CONST, infile, IsLocalId(), CSeq_inst::IsNa(), ITERATE, kStart(), NPOS, SDataLoaderConfig::OptimizeForWholeLargeSequenceRetrieval(), CSeq_id::PreferAccessionOverGi(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, TSeqLocVector2Bioseqs(), and dtl::version.

◆ BOOST_AUTO_TEST_CASE() [70/96]

BOOST_AUTO_TEST_CASE ( ReadSingleAccession_RetrieveLargeSequenceWithRange  )

Definition at line 1078 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Other, eNa_strand_both, CSeq_inst_Base::eRepr_raw, CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), infile, IsLocalId(), CSeq_inst::IsNa(), kStart(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRange(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [71/96]

BOOST_AUTO_TEST_CASE ( ReadSingleFasta_WithTitle  )

Definition at line 727 of file blastinput_unit_test.cpp.

References CRef< C, Locker >::Empty(), CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), CSeqdesc_Base::GetTitle(), infile, CSeqdesc_Base::IsTitle(), ITERATE, kFileName, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [72/96]

BOOST_AUTO_TEST_CASE ( ReadSingleGi  )

Definition at line 1263 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Gi, eNa_strand_both, CSeq_inst_Base::eRepr_raw, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), GI_CONST, infile, IsLocalId(), CSeq_inst::IsNa(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [73/96]

BOOST_AUTO_TEST_CASE ( ReadSinglePdb  )

Definition at line 2519 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Pdb, eNa_strand_unknown, CSeq_inst_Base::eRepr_raw, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), CSeq_inst::IsNa(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [74/96]

BOOST_AUTO_TEST_CASE ( ReadSinglePdb_InDifferentFormats  )

Definition at line 2651 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_Pdb, eNa_strand_unknown, CSeq_inst_Base::eRepr_raw, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), i, CSeq_inst::IsNa(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [75/96]

BOOST_AUTO_TEST_CASE ( ReadSingleTi  )

Definition at line 1524 of file blastinput_unit_test.cpp.

References b, CSeq_id_Base::e_General, eNa_strand_both, CSeq_inst_Base::eRepr_raw, CObjectManager::GetInstance(), CScope::GetObjectManager(), CBioseq_set_Base::GetSeq_set(), infile, IsLocalId(), CSeq_inst::IsNa(), SDataLoaderConfig::m_BlastDbName, CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetDataLoaderConfig(), CBlastInputSourceConfig::SetRetrieveSeqData(), rapidjson::source, and TSeqLocVector2Bioseqs().

◆ BOOST_AUTO_TEST_CASE() [76/96]

BOOST_AUTO_TEST_CASE ( RpsBlastCBS  )

Definition at line 3296 of file blastinput_unit_test.cpp.

References CBlastOptions::GetCompositionBasedStats(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetSegFiltering(), and CBlastAppArgs::SetOptions().

◆ BOOST_AUTO_TEST_CASE() [77/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_CFastaReaderNoDeflineNoNewLines  )

Definition at line 792 of file blastinput_unit_test.cpp.

References s_ReadAndTestQueryFromString_CFastaReader().

◆ BOOST_AUTO_TEST_CASE() [78/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_CFastaReaderNoNewLineAfterSeq  )

Definition at line 780 of file blastinput_unit_test.cpp.

References s_ReadAndTestQueryFromString_CFastaReader().

◆ BOOST_AUTO_TEST_CASE() [79/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_CFastaReaderWithNewLines  )

Definition at line 786 of file blastinput_unit_test.cpp.

References s_ReadAndTestQueryFromString_CFastaReader().

◆ BOOST_AUTO_TEST_CASE() [80/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_NoDeflineNoNewLines  )

Definition at line 844 of file blastinput_unit_test.cpp.

References s_ReadAndTestQueryFromString().

◆ BOOST_AUTO_TEST_CASE() [81/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_NoNewLineAfterSeq  )

Definition at line 830 of file blastinput_unit_test.cpp.

References s_ReadAndTestQueryFromString().

◆ BOOST_AUTO_TEST_CASE() [82/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_WithNewLines  )

Definition at line 837 of file blastinput_unit_test.cpp.

References s_ReadAndTestQueryFromString().

◆ BOOST_AUTO_TEST_CASE() [83/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromASN1  )

Definition at line 3092 of file blastinput_unit_test.cpp.

References count, eFirstSegment, eLastSegment, expected, flags, CBioseq_set_Base::GetSeq_set(), input(), NStr::IntToString(), and s_GetSegmentFlags().

◆ BOOST_AUTO_TEST_CASE() [84/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromFasta  )

Definition at line 2903 of file blastinput_unit_test.cpp.

References count, CShortReadFastaInputSource::eFasta, eFirstSegment, eLastSegment, expected, flags, CBioseq_set_Base::GetSeq_set(), input(), NStr::IntToString(), s_GetSegmentFlags(), and s_GetSequenceId().

◆ BOOST_AUTO_TEST_CASE() [85/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromFastC  )

Definition at line 3167 of file blastinput_unit_test.cpp.

References count, CShortReadFastaInputSource::eFastc, eFirstSegment, eLastSegment, expected, flags, CBioseq_set_Base::GetSeq_set(), input(), NStr::IntToString(), s_GetSegmentFlags(), and s_GetSequenceId().

◆ BOOST_AUTO_TEST_CASE() [86/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromFastQ  )

Definition at line 3014 of file blastinput_unit_test.cpp.

References count, CShortReadFastaInputSource::eFastq, eFirstSegment, eLastSegment, expected, flags, CBioseq_set_Base::GetSeq_set(), input(), NStr::IntToString(), s_GetSegmentFlags(), and s_GetSequenceId().

◆ BOOST_AUTO_TEST_CASE() [87/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromTwoASN1Files  )

Definition at line 3127 of file blastinput_unit_test.cpp.

References count, eFirstSegment, eLastSegment, expected, flags, CBioseq_set_Base::GetSeq_set(), input(), NStr::IntToString(), and s_GetSegmentFlags().

◆ BOOST_AUTO_TEST_CASE() [88/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromTwoFastaFiles  )

Definition at line 2942 of file blastinput_unit_test.cpp.

References count, CShortReadFastaInputSource::eFasta, eFirstSegment, eLastSegment, expected, flags, CBioseq_set_Base::GetSeq_set(), input(), NStr::IntToString(), s_GetSegmentFlags(), and s_GetSequenceId().

◆ BOOST_AUTO_TEST_CASE() [89/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromTwoFastQFiles  )

Definition at line 3052 of file blastinput_unit_test.cpp.

References count, CShortReadFastaInputSource::eFastq, eFirstSegment, eLastSegment, expected, flags, CBioseq_set_Base::GetSeq_set(), input(), NStr::IntToString(), s_GetSegmentFlags(), and s_GetSequenceId().

◆ BOOST_AUTO_TEST_CASE() [90/96]

BOOST_AUTO_TEST_CASE ( TestSingleReadsFromFasta  )

Definition at line 2982 of file blastinput_unit_test.cpp.

References count, CShortReadFastaInputSource::eFasta, expected, flags, CBioseq_set_Base::GetSeq_set(), input(), NStr::IntToString(), s_GetSegmentFlags(), and s_GetSequenceId().

◆ BOOST_AUTO_TEST_CASE() [91/96]

BOOST_AUTO_TEST_CASE ( TestSmallDubiousSequences  )

Definition at line 225 of file blastinput_unit_test.cpp.

References CSeq_inst_Base::eMol_aa, CInputException::eSequenceMismatch, CException::GetErrCode(), CObjectManager::GetInstance(), GetLength(), CScope::GetObjectManager(), IsLocalId(), ITERATE, msg(), NPOS, om, CObjectManager::RevokeAllDataLoaders(), CBlastInputSourceConfig::SetSeqLenThreshold2Guess(), rapidjson::source, and CException::what().

◆ BOOST_AUTO_TEST_CASE() [92/96]

BOOST_AUTO_TEST_CASE ( ThrowOnEmptySequence  )

Definition at line 2571 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [93/96]

BOOST_AUTO_TEST_CASE ( wb325_1  )

Definition at line 2442 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), input(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [94/96]

BOOST_AUTO_TEST_CASE ( wb325_2  )

Definition at line 2460 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), input(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [95/96]

BOOST_AUTO_TEST_CASE ( wb325_single1  )

Definition at line 2479 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), input(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE() [96/96]

BOOST_AUTO_TEST_CASE ( wb325_single2  )

Definition at line 2499 of file blastinput_unit_test.cpp.

References CObjectManager::GetInstance(), CScope::GetObjectManager(), input(), CObjectManager::RevokeAllDataLoaders(), s_DeclareBlastInput(), CBlastInputSourceConfig::SetRetrieveSeqData(), and rapidjson::source.

◆ BOOST_AUTO_TEST_CASE_TIMEOUT() [1/2]

BOOST_AUTO_TEST_CASE_TIMEOUT ( ReadSingleAccession_RetrieveLargeSequence  ,
kTimeOutLargeSeq   
)

◆ BOOST_AUTO_TEST_CASE_TIMEOUT() [2/2]

BOOST_AUTO_TEST_CASE_TIMEOUT ( ReadSingleAccession_RetrieveLargeSequenceWithRange  ,
kTimeOutLargeSeqWithRange   
)

◆ BOOST_AUTO_TEST_SUITE_END() [1/2]

BOOST_AUTO_TEST_SUITE_END ( )

Auxiliary class to convert a string into an argument count and vector.

Definition at line 3204 of file blastinput_unit_test.cpp.

References i, remove_if(), CBlastAppArgs::SetCommandLine(), NStr::Split(), and str().

◆ BOOST_AUTO_TEST_SUITE_END() [2/2]

BOOST_AUTO_TEST_SUITE_END ( ) const &

Definition at line 2852 of file blastinput_unit_test.cpp.

References CSeqdesc_Base::e_User, CUser_field_Base::GetData(), CUser_field::GetField(), CUser_field_Base::C_Data::GetInt(), and CUser_field_Base::C_Data::IsInt().

◆ s_DeclareBlastInput() [1/2]

static CRef<CBlastInput> s_DeclareBlastInput ( CNcbiIstream &  input_file,
const CBlastInputSourceConfig &  iconfig,
int  batch_size = kMax_Int 
)
static

Definition at line 78 of file blastinput_unit_test.cpp.

References input_file.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_DeclareBlastInput() [2/2]

static CRef<CBlastInput> s_DeclareBlastInput ( const string &  user_input,
const CBlastInputSourceConfig &  iconfig 
)
static

Definition at line 88 of file blastinput_unit_test.cpp.

◆ s_FileContents2String()

static string* s_FileContents2String ( const char *  file_name)
static

Definition at line 1665 of file blastinput_unit_test.cpp.

References buffer, file, file_name, and string.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_GetSequenceId()

static string s_GetSequenceId ( const CBioseq &  bioseq)
static

Definition at line 2882 of file blastinput_unit_test.cpp.

References CSeq_id::AsFastaString(), CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq::GetFirstId(), CBioseq_Base::IsSetDescr(), NStr::Split(), and string.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_Ignore()

template<typename T >
void s_Ignore ( const T &  )
inline

Definition at line 2757 of file blastinput_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_ReadAndTestQueryFromString()

static void s_ReadAndTestQueryFromString ( const string &  input,
TSeqPos  expected_length,
bool  is_protein 
)
static

Definition at line 800 of file blastinput_unit_test.cpp.

References CBlastInput::GetAllSeqLocs(), CObjectManager::GetInstance(), GetLength(), CScope::GetObjectManager(), input(), CSeqVector::IsProtein(), msg(), query, CObjectManager::RevokeAllDataLoaders(), CSeqVector::SetIupacCoding(), and CSeqVector::size().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_ReadAndTestQueryFromString_CFastaReader()

static void s_ReadAndTestQueryFromString_CFastaReader ( const string &  input,
TSeqPos  expected_length 
)
static

Definition at line 756 of file blastinput_unit_test.cpp.

References ILineError::eProblem_ModifierFoundButNoneExpected, ILineError::eProblem_TooLong, CFastaReader::fAssumeNuc, CFastaReader::fDisableNoResidues, CFastaReader::fDLOptional, CFastaReader::fHyphensIgnoreAndWarn, CFastaReader::fNoParseID, CFastaReader::fNoSplit, CFastaReader::fQuickIDCheck, CBioseq::GetLength(), CSeq_entry_Base::GetSeq(), CFastaReader::IgnoreProblem(), input(), kEmptyStr, CFastaReader::ReadOneSeq(), and CFastaReader::SetIDGenerator().

Referenced by BOOST_AUTO_TEST_CASE().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )

Variable Documentation

◆ kTimeOutLargeSeq

const int kTimeOutLargeSeq = 60

Definition at line 1071 of file blastinput_unit_test.cpp.

◆ kTimeOutLargeSeqWithRange

const int kTimeOutLargeSeqWithRange = 60

Definition at line 1132 of file blastinput_unit_test.cpp.

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 73 of file blastinput_unit_test.cpp.

Generated by doxygen 1.9.0
Modified on Fri Sep 20 14:57:23 2024 by modify_doxy.py rev. 669887