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.

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Classes

struct  SDubiousShortSequence
 

Functions

 USING_SCOPE (blast)
 
 USING_SCOPE (objects)
 
static CRef< CBlastInputs_DeclareBlastInput (CNcbiIstream &input_file, const CBlastInputSourceConfig &iconfig, int batch_size=kMax_Int)
 
static CRef< CBlastInputs_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 strings_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  )

◆ 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  )

◆ BOOST_AUTO_TEST_CASE() [11/96]

BOOST_AUTO_TEST_CASE ( FetchGiFromAccessionInput  )

◆ BOOST_AUTO_TEST_CASE() [12/96]

BOOST_AUTO_TEST_CASE ( FetchSraID  )

◆ BOOST_AUTO_TEST_CASE() [13/96]

BOOST_AUTO_TEST_CASE ( MultiBatch  )

◆ BOOST_AUTO_TEST_CASE() [14/96]

BOOST_AUTO_TEST_CASE ( MultiRange  )

◆ BOOST_AUTO_TEST_CASE() [15/96]

BOOST_AUTO_TEST_CASE ( MultiSeq  )

◆ BOOST_AUTO_TEST_CASE() [16/96]

BOOST_AUTO_TEST_CASE ( NoDeflineExpected  )

◆ BOOST_AUTO_TEST_CASE() [17/96]

BOOST_AUTO_TEST_CASE ( NoDeflineUnexpected  )

◆ BOOST_AUTO_TEST_CASE() [18/96]

BOOST_AUTO_TEST_CASE ( NuclLcaseMask_BlastQueryVector  )

◆ BOOST_AUTO_TEST_CASE() [19/96]

BOOST_AUTO_TEST_CASE ( NuclLcaseMask_TSeqLocVector  )

◆ BOOST_AUTO_TEST_CASE() [20/96]

BOOST_AUTO_TEST_CASE ( NuclStrand  )

◆ BOOST_AUTO_TEST_CASE() [21/96]

BOOST_AUTO_TEST_CASE ( ParseDefline  )

◆ 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(), and r().

◆ 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  )

◆ BOOST_AUTO_TEST_CASE() [29/96]

BOOST_AUTO_TEST_CASE ( RangeBoth  )

◆ BOOST_AUTO_TEST_CASE() [30/96]

BOOST_AUTO_TEST_CASE ( RangeInvalid_FromGreaterThanSequenceLength  )

◆ BOOST_AUTO_TEST_CASE() [31/96]

BOOST_AUTO_TEST_CASE ( RangeInvalid_FromGreaterThanTo  )

◆ BOOST_AUTO_TEST_CASE() [32/96]

BOOST_AUTO_TEST_CASE ( RangeInvalid_ToEqualThanSequenceLength  )

◆ BOOST_AUTO_TEST_CASE() [33/96]

BOOST_AUTO_TEST_CASE ( RangeInvalid_ToGreaterThanSequenceLength  )

◆ BOOST_AUTO_TEST_CASE() [34/96]

BOOST_AUTO_TEST_CASE ( RangeStartOnly  )

◆ BOOST_AUTO_TEST_CASE() [35/96]

BOOST_AUTO_TEST_CASE ( RawFastaNoSpaces  )

◆ BOOST_AUTO_TEST_CASE() [36/96]

BOOST_AUTO_TEST_CASE ( RawFastaNoSpaces_UpperCaseWithN  )

◆ BOOST_AUTO_TEST_CASE() [37/96]

BOOST_AUTO_TEST_CASE ( RawFastaNoSpaces_UpperCaseWithN_ReadDeltaSeq  )

◆ BOOST_AUTO_TEST_CASE() [38/96]

BOOST_AUTO_TEST_CASE ( RawFastaWithSpaces  )

◆ BOOST_AUTO_TEST_CASE() [39/96]

BOOST_AUTO_TEST_CASE ( ReadAccession_MismatchNuclProt  )

◆ BOOST_AUTO_TEST_CASE() [40/96]

BOOST_AUTO_TEST_CASE ( ReadAccession_MismatchProtNucl  )

◆ BOOST_AUTO_TEST_CASE() [41/96]

BOOST_AUTO_TEST_CASE ( ReadAccessionNucleotideIntoBuffer_Single  )

◆ BOOST_AUTO_TEST_CASE() [42/96]

BOOST_AUTO_TEST_CASE ( ReadAccessionNuclWithFlankingSpacesIntoBuffer_Single  )

◆ BOOST_AUTO_TEST_CASE() [43/96]

BOOST_AUTO_TEST_CASE ( ReadAccessionsAndGisWithNewLines  )

◆ BOOST_AUTO_TEST_CASE() [44/96]

BOOST_AUTO_TEST_CASE ( ReadBadUserInput  )

◆ BOOST_AUTO_TEST_CASE() [45/96]

BOOST_AUTO_TEST_CASE ( ReadEmptyUserInput  )

◆ BOOST_AUTO_TEST_CASE() [46/96]

BOOST_AUTO_TEST_CASE ( ReadEmptyUserInput_OnlyTitle  )

◆ BOOST_AUTO_TEST_CASE() [47/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDefline_MismatchNuclProt  )

◆ BOOST_AUTO_TEST_CASE() [48/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDefline_MismatchProtNucl  )

◆ BOOST_AUTO_TEST_CASE() [49/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDeflineNucl_Multiple  )

◆ BOOST_AUTO_TEST_CASE() [50/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDeflineProtein_Single  )

◆ BOOST_AUTO_TEST_CASE() [51/96]

BOOST_AUTO_TEST_CASE ( ReadFastaWithDeflineProteinIntoBuffer_Single  )

◆ BOOST_AUTO_TEST_CASE() [52/96]

BOOST_AUTO_TEST_CASE ( ReadGenbankReport  )

◆ BOOST_AUTO_TEST_CASE() [53/96]

BOOST_AUTO_TEST_CASE ( ReadGi_MismatchNuclProt  )

◆ BOOST_AUTO_TEST_CASE() [54/96]

BOOST_AUTO_TEST_CASE ( ReadGi_MismatchProtNucl  )

◆ BOOST_AUTO_TEST_CASE() [55/96]

BOOST_AUTO_TEST_CASE ( ReadGiNuclWithFlankingSpacesIntoBuffer_Single  )

◆ BOOST_AUTO_TEST_CASE() [56/96]

BOOST_AUTO_TEST_CASE ( ReadInvalidGi  )

◆ BOOST_AUTO_TEST_CASE() [57/96]

BOOST_AUTO_TEST_CASE ( ReadInvalidSeqId  )

◆ BOOST_AUTO_TEST_CASE() [58/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleAccessions  )

◆ BOOST_AUTO_TEST_CASE() [59/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleAccessionsFromMemory  )

◆ BOOST_AUTO_TEST_CASE() [60/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleGis  )

◆ BOOST_AUTO_TEST_CASE() [61/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleGis_WithBadInput  )

◆ BOOST_AUTO_TEST_CASE() [62/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleSequences_OneEmpty  )

◆ BOOST_AUTO_TEST_CASE() [63/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleSequencesFromSequencer  )

◆ BOOST_AUTO_TEST_CASE() [64/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleSequencesFromSequencerParseLocalIds  )

◆ BOOST_AUTO_TEST_CASE() [65/96]

BOOST_AUTO_TEST_CASE ( ReadMultipleTis  )

◆ BOOST_AUTO_TEST_CASE() [66/96]

BOOST_AUTO_TEST_CASE ( ReadProteinWithGaps  )

◆ BOOST_AUTO_TEST_CASE() [67/96]

BOOST_AUTO_TEST_CASE ( ReadSequenceWithlclID  )

◆ BOOST_AUTO_TEST_CASE() [68/96]

BOOST_AUTO_TEST_CASE ( ReadSingleAccession  )

◆ BOOST_AUTO_TEST_CASE() [69/96]

BOOST_AUTO_TEST_CASE ( ReadSingleAccession_RetrieveLargeSequence  )

◆ BOOST_AUTO_TEST_CASE() [70/96]

BOOST_AUTO_TEST_CASE ( ReadSingleAccession_RetrieveLargeSequenceWithRange  )

◆ BOOST_AUTO_TEST_CASE() [71/96]

BOOST_AUTO_TEST_CASE ( ReadSingleFasta_WithTitle  )

◆ BOOST_AUTO_TEST_CASE() [72/96]

BOOST_AUTO_TEST_CASE ( ReadSingleGi  )

◆ BOOST_AUTO_TEST_CASE() [73/96]

BOOST_AUTO_TEST_CASE ( ReadSinglePdb  )

◆ BOOST_AUTO_TEST_CASE() [74/96]

BOOST_AUTO_TEST_CASE ( ReadSinglePdb_InDifferentFormats  )

◆ BOOST_AUTO_TEST_CASE() [75/96]

BOOST_AUTO_TEST_CASE ( ReadSingleTi  )

◆ BOOST_AUTO_TEST_CASE() [76/96]

BOOST_AUTO_TEST_CASE ( RpsBlastCBS  )

◆ BOOST_AUTO_TEST_CASE() [77/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_CFastaReaderNoDeflineNoNewLines  )

◆ BOOST_AUTO_TEST_CASE() [78/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_CFastaReaderNoNewLineAfterSeq  )

◆ BOOST_AUTO_TEST_CASE() [79/96]

BOOST_AUTO_TEST_CASE ( SingleSequenceString_CFastaReaderWithNewLines  )

◆ 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  )

◆ BOOST_AUTO_TEST_CASE() [84/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromFasta  )

◆ BOOST_AUTO_TEST_CASE() [85/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromFastC  )

◆ BOOST_AUTO_TEST_CASE() [86/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromFastQ  )

◆ BOOST_AUTO_TEST_CASE() [87/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromTwoASN1Files  )

◆ BOOST_AUTO_TEST_CASE() [88/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromTwoFastaFiles  )

◆ BOOST_AUTO_TEST_CASE() [89/96]

BOOST_AUTO_TEST_CASE ( TestPairedReadsFromTwoFastQFiles  )

◆ BOOST_AUTO_TEST_CASE() [90/96]

BOOST_AUTO_TEST_CASE ( TestSingleReadsFromFasta  )

◆ BOOST_AUTO_TEST_CASE() [91/96]

BOOST_AUTO_TEST_CASE ( TestSmallDubiousSequences  )

◆ BOOST_AUTO_TEST_CASE() [92/96]

BOOST_AUTO_TEST_CASE ( ThrowOnEmptySequence  )

◆ BOOST_AUTO_TEST_CASE() [93/96]

BOOST_AUTO_TEST_CASE ( wb325_1  )

◆ BOOST_AUTO_TEST_CASE() [94/96]

BOOST_AUTO_TEST_CASE ( wb325_2  )

◆ BOOST_AUTO_TEST_CASE() [95/96]

BOOST_AUTO_TEST_CASE ( wb325_single1  )

◆ BOOST_AUTO_TEST_CASE() [96/96]

BOOST_AUTO_TEST_CASE ( wb325_single2  )

◆ 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 &

◆ 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

◆ 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

◆ s_ReadAndTestQueryFromString_CFastaReader()

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

◆ 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.

Modified on Sun May 19 04:46:27 2024 by modify_doxy.py rev. 669887