NCBI C++ ToolKit
Macros | Enumerations | Functions | Variables
bl2seq_unit_test.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/general/Object_id.hpp>
#include <serial/serial.hpp>
#include <serial/iterator.hpp>
#include <serial/objostr.hpp>
#include <algo/blast/api/tblastn_options.hpp>
#include <algo/blast/format/blastfmtutil.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/blast_prot_options.hpp>
#include <algo/blast/api/blastx_options.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/disc_nucl_options.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/api/local_db_adapter.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/blastinput/blast_input.hpp>
#include <algo/blast/blastinput/blast_fasta_input.hpp>
#include <algo/blast/api/windowmask_filter.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/simple/simple_om.hpp>
#include <objtools/readers/fasta.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objmgr/util/sequence.hpp>
#include "test_objmgr.hpp"
#include <util/random_gen.hpp>
+ Include dependency graph for bl2seq_unit_test.cpp:

Go to the source code of this file.

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Macros

#define ARRAY_SIZE(a)   (sizeof(a)/sizeof(*a))
 

Enumerations

enum  EBl2seqTest {
  eBlastp_129295_129295 = 0 , eBlastn_555_555 , eMegablast_555_555 , eDiscMegablast_555_555 ,
  eBlastx_555_129295 , eTblastn_129295_555 , eTblastn_129295_555_large_word , eTblastx_555_555 ,
  eTblastx_many_hits , eBlastp_129295_7662354 , eBlastn_555_3090 , eBlastp_multi_q ,
  eBlastn_multi_q , eBlastp_multi_q_s , eTblastn_oof , eBlastx_oof ,
  eDiscMegablast_U02544_U61969 , eMegablast_chrom_mrna
}
 

Functions

 USING_SCOPE (blast)
 
 USING_SCOPE (objects)
 
CRef< CSeq_locs_MakePackedInt2 (CRef< CSeq_id > id, vector< TSeqRange > &range_vec)
 
 BOOST_AUTO_TEST_CASE (NucleotideMultipleSeqLocs1)
 
 BOOST_AUTO_TEST_CASE (ProteinBlastInvalidSeqIdSelfHit)
 
Boolean interrupt_immediately (SBlastProgress *)
 Returns true so that the processing stops upon the first invocation of this callback. More...
 
Boolean do_not_interrupt (SBlastProgress *)
 Returns false so that the processing never stops in spite of a callback function to interrupt the process is provided. More...
 
Boolean callback_counter (SBlastProgress *progress_info)
 This callback never interrupts the BLAST search, its only purpose is to count the number of times this is invoked for the given input. More...
 
Boolean interrupt_at_random (SBlastProgress *progress_info)
 This callback interrupts the BLAST search after the callback has been executed the requested number of times in the pair's second member. More...
 
Boolean interrupt_after3calls (SBlastProgress *)
 The interruption occurs after 3 invokations of this callback. More...
 
Boolean interrupt_on_traceback (SBlastProgress *progress_info)
 The interruption occurs after starting the traceback stage. More...
 
void testRawCutoffs (CBl2Seq &blaster, EProgram program, EBl2seqTest test_id)
 
void testResultAlignments (size_t num_queries, size_t num_subjects, TSeqAlignVector result_alnvec)
 
void testBlastHitCounts (CBl2Seq &blaster, EBl2seqTest test_id)
 
 BOOST_AUTO_TEST_CASE (ProteinBlastSelfHit)
 
 BOOST_AUTO_TEST_CASE (TBlastn2Seqs)
 
 BOOST_AUTO_TEST_CASE (TBlastn2SeqsRevStrand1)
 
 BOOST_AUTO_TEST_CASE (TBlastn2SeqsRevStrand2)
 
 BOOST_AUTO_TEST_CASE (TBlastn2SeqsCompBasedStats)
 
 BOOST_AUTO_TEST_CASE (TBlastn2SeqsLargeWord)
 
 BOOST_AUTO_TEST_CASE (IdenticalProteins)
 
 BOOST_AUTO_TEST_CASE (UnsupportedOption)
 
 BOOST_AUTO_TEST_CASE (PositiveMismatchOption)
 
 BOOST_AUTO_TEST_CASE (FullyMaskedSequence)
 
 BOOST_AUTO_TEST_CASE (MultipleQueries1FullyMasked)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastpExitImmediately)
 
 BOOST_AUTO_TEST_CASE (Tblastn2Seqs_PlusStrandOnly)
 
 BOOST_AUTO_TEST_CASE_TIMEOUT (testInterruptBlastSetup, 3)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastSetup)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastnExitImmediately)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastxExitImmediately)
 
 BOOST_AUTO_TEST_CASE (testInterruptTblastxExitImmediately)
 
 BOOST_AUTO_TEST_CASE (testInterruptTblastnExitImmediately)
 
static CRef< CBl2Seqs_SetupWithMultipleQueriesAndSubjects (bool query_is_nucl, bool subj_is_nucl, EProgram program)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastpExitAtRandom)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastnExitAtRandom)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastxExitAtRandom)
 
 BOOST_AUTO_TEST_CASE (testInterruptTblastnExitAtRandom)
 
 BOOST_AUTO_TEST_CASE (testInterruptTblastxExitAtRandom)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastpExitAfter3Callbacks)
 
 BOOST_AUTO_TEST_CASE (testInterruptBlastxExitOnTraceback)
 
 BOOST_AUTO_TEST_CASE (testInterruptTblastxExitOnTraceback)
 
 BOOST_AUTO_TEST_CASE (ProteinBlastMultipleQueriesWithInvalidSeqId)
 
 BOOST_AUTO_TEST_CASE (ProteinBlastMultipleQueriesWithBadQuery)
 
 BOOST_AUTO_TEST_CASE (NucleotideBlastMultipleQueriesWithInvalidSeqId)
 
 BOOST_AUTO_TEST_CASE (ProteinSelfHitWithMask)
 
 BOOST_AUTO_TEST_CASE (NucleotideMaskedLocation)
 
 BOOST_AUTO_TEST_CASE (NucleotideMaskedLocation_FromFile)
 
 BOOST_AUTO_TEST_CASE (InvalidMaskingAlgorithm)
 
 BOOST_AUTO_TEST_CASE (ProteinCompBasedStats)
 
 BOOST_AUTO_TEST_CASE (Blastx2Seqs_QueryBothStrands)
 
 BOOST_AUTO_TEST_CASE (NucleotideSelfHitWithSubjectMask)
 
 BOOST_AUTO_TEST_CASE (NucleotideBlastSelfHit)
 
 BOOST_AUTO_TEST_CASE (MegablastGreedyTraceback)
 
 BOOST_AUTO_TEST_CASE (MegablastGreedyTraceback2)
 
 BOOST_AUTO_TEST_CASE (MegablastGreedyTracebackSelfHits)
 
 BOOST_AUTO_TEST_CASE (Blastx2Seqs_QueryPlusStrand)
 
 BOOST_AUTO_TEST_CASE (Blastx2Seqs_QueryMinusStrand)
 
 BOOST_AUTO_TEST_CASE (TBlastx2Seqs_QueryBothStrands)
 
 BOOST_AUTO_TEST_CASE (TBlastx2Seqs_QueryPlusStrand)
 
 BOOST_AUTO_TEST_CASE (TBlastx2Seqs_QueryMinusStrand)
 
 BOOST_AUTO_TEST_CASE (TblastxManyHits)
 
 BOOST_AUTO_TEST_CASE (ProteinBlast2Seqs)
 
 BOOST_AUTO_TEST_CASE (BlastnWithRepeatFiltering_InvalidDB)
 
 BOOST_AUTO_TEST_CASE (BlastnWithRepeatFiltering)
 
 BOOST_AUTO_TEST_CASE (BlastnWithWindowMasker_Db)
 
 BOOST_AUTO_TEST_CASE (BlastnWithWindowMasker_Taxid)
 
 BOOST_AUTO_TEST_CASE (BlastnWithWindowMasker_InvalidDb)
 
 BOOST_AUTO_TEST_CASE (BlastnWithWindowMasker_InvalidTaxid)
 
 BOOST_AUTO_TEST_CASE (WindowMaskerPathInitInvalid)
 
 BOOST_AUTO_TEST_CASE (WindowMaskerPathInitValid)
 
 BOOST_AUTO_TEST_CASE (BlastnWithWindowMasker_DbAndTaxid)
 
 BOOST_AUTO_TEST_CASE (ConvertTaxIdToWindowMaskerDb)
 
 BOOST_AUTO_TEST_CASE (Alex)
 
 BOOST_AUTO_TEST_CASE (NucleotideBlast2Seqs)
 
 BOOST_AUTO_TEST_CASE (ProteinBlastChangeQuery)
 
 BOOST_AUTO_TEST_CASE (ProteinBlastChangeSubject)
 
 BOOST_AUTO_TEST_CASE (NucleotideBlastChangeQuery)
 
 BOOST_AUTO_TEST_CASE (NucleotideBlastChangeSubject)
 
 BOOST_AUTO_TEST_CASE (ProteinBlastMultipleQueries)
 
 BOOST_AUTO_TEST_CASE (NucleotideBlastMultipleQueries)
 
 BOOST_AUTO_TEST_CASE (TblastnOutOfFrame)
 
 BOOST_AUTO_TEST_CASE (TblastnOutOfFrame2)
 
 BOOST_AUTO_TEST_CASE (BlastxOutOfFrame)
 
 BOOST_AUTO_TEST_CASE (BlastxOutOfFrame_DifferentFrames)
 
void x_TestAlignmentQuerySubjStrandCombinations (TSeqAlignVector &sav, string aligned_strands)
 
static void testIntervalWholeAlignment (TSeqAlignVector &sav)
 
static void testWholeIntervalAlignment (TSeqAlignVector &sav)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryBothStrands_SubjBothStrands)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryBothStrands_SubjPlusStrand)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryBothStrands_SubjMinusStrand)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryPlusStrand_SubjPlusStrand)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryPlusStrand_SubjMinusStrand)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryPlusStrand_SubjBothStrands)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryMinusStrand_SubjMinusStrand)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryMinusStrand_SubjPlusStrand)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryMinusStrand_SubjBothStrands)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryWhole_SubjInterval)
 
 BOOST_AUTO_TEST_CASE (Blastn_QueryInterval_SubjWhole)
 
 BOOST_AUTO_TEST_CASE (BlastpMultipleQueries_MultipleSubjs)
 
 BOOST_AUTO_TEST_CASE (BlastpMultipleQueries_MultipleSubjs_RunEx)
 
 BOOST_AUTO_TEST_CASE (BlastpMultipleQueries_MultipleSubjs_CLocalBlast)
 
 BOOST_AUTO_TEST_CASE (Blastp_MultipleSubjs_SearchAsSet)
 
 BOOST_AUTO_TEST_CASE (BlastOptionsEquality)
 
 BOOST_AUTO_TEST_CASE (BlastOptionsInequality)
 
 BOOST_AUTO_TEST_CASE (DiscontiguousMB)
 
 BOOST_AUTO_TEST_CASE (BlastnHumanChrom_MRNA)
 
 BOOST_AUTO_TEST_CASE (testOneSubjectResults2CSeqAlign)
 
 BOOST_AUTO_TEST_CASE (testMultiSeqSearchSymmetry)
 
 BOOST_AUTO_TEST_CASE (testInterruptCallbackWithNull)
 
 BOOST_AUTO_TEST_CASE (testInterruptCallbackDoNotInterrupt)
 
 BOOST_AUTO_TEST_CASE (QueryMaskIgnoredInMiniExtension)
 

Variables

 USING_NCBI_SCOPE
 

Macro Definition Documentation

◆ ARRAY_SIZE

#define ARRAY_SIZE (   a)    (sizeof(a)/sizeof(*a))

Definition at line 1082 of file bl2seq_unit_test.cpp.

Enumeration Type Documentation

◆ EBl2seqTest

Enumerator
eBlastp_129295_129295 
eBlastn_555_555 
eMegablast_555_555 
eDiscMegablast_555_555 
eBlastx_555_129295 
eTblastn_129295_555 
eTblastn_129295_555_large_word 
eTblastx_555_555 
eTblastx_many_hits 
eBlastp_129295_7662354 
eBlastn_555_3090 
eBlastp_multi_q 
eBlastn_multi_q 
eBlastp_multi_q_s 
eTblastn_oof 
eBlastx_oof 
eDiscMegablast_U02544_U61969 
eMegablast_chrom_mrna 

Definition at line 171 of file bl2seq_unit_test.cpp.

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/95]

BOOST_AUTO_TEST_CASE ( Alex  )

◆ BOOST_AUTO_TEST_CASE() [2/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryBothStrands_SubjBothStrands  )

◆ BOOST_AUTO_TEST_CASE() [3/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryBothStrands_SubjMinusStrand  )

◆ BOOST_AUTO_TEST_CASE() [4/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryBothStrands_SubjPlusStrand  )

◆ BOOST_AUTO_TEST_CASE() [5/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryInterval_SubjWhole  )

◆ BOOST_AUTO_TEST_CASE() [6/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryMinusStrand_SubjBothStrands  )

◆ BOOST_AUTO_TEST_CASE() [7/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryMinusStrand_SubjMinusStrand  )

◆ BOOST_AUTO_TEST_CASE() [8/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryMinusStrand_SubjPlusStrand  )

◆ BOOST_AUTO_TEST_CASE() [9/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryPlusStrand_SubjBothStrands  )

◆ BOOST_AUTO_TEST_CASE() [10/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryPlusStrand_SubjMinusStrand  )

◆ BOOST_AUTO_TEST_CASE() [11/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryPlusStrand_SubjPlusStrand  )

◆ BOOST_AUTO_TEST_CASE() [12/95]

BOOST_AUTO_TEST_CASE ( Blastn_QueryWhole_SubjInterval  )

◆ BOOST_AUTO_TEST_CASE() [13/95]

BOOST_AUTO_TEST_CASE ( BlastnHumanChrom_MRNA  )

◆ BOOST_AUTO_TEST_CASE() [14/95]

BOOST_AUTO_TEST_CASE ( BlastnWithRepeatFiltering  )

◆ BOOST_AUTO_TEST_CASE() [15/95]

BOOST_AUTO_TEST_CASE ( BlastnWithRepeatFiltering_InvalidDB  )

◆ BOOST_AUTO_TEST_CASE() [16/95]

BOOST_AUTO_TEST_CASE ( BlastnWithWindowMasker_Db  )

◆ BOOST_AUTO_TEST_CASE() [17/95]

BOOST_AUTO_TEST_CASE ( BlastnWithWindowMasker_DbAndTaxid  )

◆ BOOST_AUTO_TEST_CASE() [18/95]

BOOST_AUTO_TEST_CASE ( BlastnWithWindowMasker_InvalidDb  )

◆ BOOST_AUTO_TEST_CASE() [19/95]

BOOST_AUTO_TEST_CASE ( BlastnWithWindowMasker_InvalidTaxid  )

◆ BOOST_AUTO_TEST_CASE() [20/95]

BOOST_AUTO_TEST_CASE ( BlastnWithWindowMasker_Taxid  )

◆ BOOST_AUTO_TEST_CASE() [21/95]

BOOST_AUTO_TEST_CASE ( BlastOptionsEquality  )

◆ BOOST_AUTO_TEST_CASE() [22/95]

BOOST_AUTO_TEST_CASE ( BlastOptionsInequality  )

◆ BOOST_AUTO_TEST_CASE() [23/95]

BOOST_AUTO_TEST_CASE ( Blastp_MultipleSubjs_SearchAsSet  )

◆ BOOST_AUTO_TEST_CASE() [24/95]

BOOST_AUTO_TEST_CASE ( BlastpMultipleQueries_MultipleSubjs  )

◆ BOOST_AUTO_TEST_CASE() [25/95]

BOOST_AUTO_TEST_CASE ( BlastpMultipleQueries_MultipleSubjs_CLocalBlast  )

◆ BOOST_AUTO_TEST_CASE() [26/95]

BOOST_AUTO_TEST_CASE ( BlastpMultipleQueries_MultipleSubjs_RunEx  )

◆ BOOST_AUTO_TEST_CASE() [27/95]

BOOST_AUTO_TEST_CASE ( Blastx2Seqs_QueryBothStrands  )

◆ BOOST_AUTO_TEST_CASE() [28/95]

BOOST_AUTO_TEST_CASE ( Blastx2Seqs_QueryMinusStrand  )

◆ BOOST_AUTO_TEST_CASE() [29/95]

BOOST_AUTO_TEST_CASE ( Blastx2Seqs_QueryPlusStrand  )

◆ BOOST_AUTO_TEST_CASE() [30/95]

BOOST_AUTO_TEST_CASE ( BlastxOutOfFrame  )

◆ BOOST_AUTO_TEST_CASE() [31/95]

BOOST_AUTO_TEST_CASE ( BlastxOutOfFrame_DifferentFrames  )

◆ BOOST_AUTO_TEST_CASE() [32/95]

BOOST_AUTO_TEST_CASE ( ConvertTaxIdToWindowMaskerDb  )

Definition at line 2147 of file bl2seq_unit_test.cpp.

References NStr::EndsWith(), and WindowMaskerTaxidToDb().

◆ BOOST_AUTO_TEST_CASE() [33/95]

BOOST_AUTO_TEST_CASE ( DiscontiguousMB  )

◆ BOOST_AUTO_TEST_CASE() [34/95]

BOOST_AUTO_TEST_CASE ( FullyMaskedSequence  )

◆ BOOST_AUTO_TEST_CASE() [35/95]

BOOST_AUTO_TEST_CASE ( IdenticalProteins  )

◆ BOOST_AUTO_TEST_CASE() [36/95]

BOOST_AUTO_TEST_CASE ( InvalidMaskingAlgorithm  )

◆ BOOST_AUTO_TEST_CASE() [37/95]

BOOST_AUTO_TEST_CASE ( MegablastGreedyTraceback  )

◆ BOOST_AUTO_TEST_CASE() [38/95]

BOOST_AUTO_TEST_CASE ( MegablastGreedyTraceback2  )

◆ BOOST_AUTO_TEST_CASE() [39/95]

BOOST_AUTO_TEST_CASE ( MegablastGreedyTracebackSelfHits  )

◆ BOOST_AUTO_TEST_CASE() [40/95]

BOOST_AUTO_TEST_CASE ( MultipleQueries1FullyMasked  )

◆ BOOST_AUTO_TEST_CASE() [41/95]

BOOST_AUTO_TEST_CASE ( NucleotideBlast2Seqs  )

◆ BOOST_AUTO_TEST_CASE() [42/95]

BOOST_AUTO_TEST_CASE ( NucleotideBlastChangeQuery  )

◆ BOOST_AUTO_TEST_CASE() [43/95]

BOOST_AUTO_TEST_CASE ( NucleotideBlastChangeSubject  )

◆ BOOST_AUTO_TEST_CASE() [44/95]

BOOST_AUTO_TEST_CASE ( NucleotideBlastMultipleQueries  )

◆ BOOST_AUTO_TEST_CASE() [45/95]

BOOST_AUTO_TEST_CASE ( NucleotideBlastMultipleQueriesWithInvalidSeqId  )

◆ BOOST_AUTO_TEST_CASE() [46/95]

BOOST_AUTO_TEST_CASE ( NucleotideBlastSelfHit  )

◆ BOOST_AUTO_TEST_CASE() [47/95]

BOOST_AUTO_TEST_CASE ( NucleotideMaskedLocation  )

◆ BOOST_AUTO_TEST_CASE() [48/95]

BOOST_AUTO_TEST_CASE ( NucleotideMaskedLocation_FromFile  )

◆ BOOST_AUTO_TEST_CASE() [49/95]

BOOST_AUTO_TEST_CASE ( NucleotideMultipleSeqLocs1  )

◆ BOOST_AUTO_TEST_CASE() [50/95]

BOOST_AUTO_TEST_CASE ( NucleotideSelfHitWithSubjectMask  )

◆ BOOST_AUTO_TEST_CASE() [51/95]

BOOST_AUTO_TEST_CASE ( PositiveMismatchOption  )

◆ BOOST_AUTO_TEST_CASE() [52/95]

BOOST_AUTO_TEST_CASE ( ProteinBlast2Seqs  )

◆ BOOST_AUTO_TEST_CASE() [53/95]

BOOST_AUTO_TEST_CASE ( ProteinBlastChangeQuery  )

◆ BOOST_AUTO_TEST_CASE() [54/95]

BOOST_AUTO_TEST_CASE ( ProteinBlastChangeSubject  )

◆ BOOST_AUTO_TEST_CASE() [55/95]

BOOST_AUTO_TEST_CASE ( ProteinBlastInvalidSeqIdSelfHit  )

◆ BOOST_AUTO_TEST_CASE() [56/95]

BOOST_AUTO_TEST_CASE ( ProteinBlastMultipleQueries  )

◆ BOOST_AUTO_TEST_CASE() [57/95]

BOOST_AUTO_TEST_CASE ( ProteinBlastMultipleQueriesWithBadQuery  )

◆ BOOST_AUTO_TEST_CASE() [58/95]

BOOST_AUTO_TEST_CASE ( ProteinBlastMultipleQueriesWithInvalidSeqId  )

◆ BOOST_AUTO_TEST_CASE() [59/95]

BOOST_AUTO_TEST_CASE ( ProteinBlastSelfHit  )

◆ BOOST_AUTO_TEST_CASE() [60/95]

BOOST_AUTO_TEST_CASE ( ProteinCompBasedStats  )

◆ BOOST_AUTO_TEST_CASE() [61/95]

BOOST_AUTO_TEST_CASE ( ProteinSelfHitWithMask  )

◆ BOOST_AUTO_TEST_CASE() [62/95]

BOOST_AUTO_TEST_CASE ( QueryMaskIgnoredInMiniExtension  )

◆ BOOST_AUTO_TEST_CASE() [63/95]

BOOST_AUTO_TEST_CASE ( TBlastn2Seqs  )

◆ BOOST_AUTO_TEST_CASE() [64/95]

BOOST_AUTO_TEST_CASE ( Tblastn2Seqs_PlusStrandOnly  )

◆ BOOST_AUTO_TEST_CASE() [65/95]

BOOST_AUTO_TEST_CASE ( TBlastn2SeqsCompBasedStats  )

◆ BOOST_AUTO_TEST_CASE() [66/95]

BOOST_AUTO_TEST_CASE ( TBlastn2SeqsLargeWord  )

◆ BOOST_AUTO_TEST_CASE() [67/95]

BOOST_AUTO_TEST_CASE ( TBlastn2SeqsRevStrand1  )

◆ BOOST_AUTO_TEST_CASE() [68/95]

BOOST_AUTO_TEST_CASE ( TBlastn2SeqsRevStrand2  )

◆ BOOST_AUTO_TEST_CASE() [69/95]

BOOST_AUTO_TEST_CASE ( TblastnOutOfFrame  )

◆ BOOST_AUTO_TEST_CASE() [70/95]

BOOST_AUTO_TEST_CASE ( TblastnOutOfFrame2  )

◆ BOOST_AUTO_TEST_CASE() [71/95]

BOOST_AUTO_TEST_CASE ( TBlastx2Seqs_QueryBothStrands  )

◆ BOOST_AUTO_TEST_CASE() [72/95]

BOOST_AUTO_TEST_CASE ( TBlastx2Seqs_QueryMinusStrand  )

◆ BOOST_AUTO_TEST_CASE() [73/95]

BOOST_AUTO_TEST_CASE ( TBlastx2Seqs_QueryPlusStrand  )

◆ BOOST_AUTO_TEST_CASE() [74/95]

BOOST_AUTO_TEST_CASE ( TblastxManyHits  )

◆ BOOST_AUTO_TEST_CASE() [75/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastnExitAtRandom  )

◆ BOOST_AUTO_TEST_CASE() [76/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastnExitImmediately  )

◆ BOOST_AUTO_TEST_CASE() [77/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastpExitAfter3Callbacks  )

◆ BOOST_AUTO_TEST_CASE() [78/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastpExitAtRandom  )

◆ BOOST_AUTO_TEST_CASE() [79/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastpExitImmediately  )

◆ BOOST_AUTO_TEST_CASE() [80/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastSetup  )

◆ BOOST_AUTO_TEST_CASE() [81/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastxExitAtRandom  )

◆ BOOST_AUTO_TEST_CASE() [82/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastxExitImmediately  )

◆ BOOST_AUTO_TEST_CASE() [83/95]

BOOST_AUTO_TEST_CASE ( testInterruptBlastxExitOnTraceback  )

◆ BOOST_AUTO_TEST_CASE() [84/95]

BOOST_AUTO_TEST_CASE ( testInterruptCallbackDoNotInterrupt  )

◆ BOOST_AUTO_TEST_CASE() [85/95]

BOOST_AUTO_TEST_CASE ( testInterruptCallbackWithNull  )

◆ BOOST_AUTO_TEST_CASE() [86/95]

BOOST_AUTO_TEST_CASE ( testInterruptTblastnExitAtRandom  )

◆ BOOST_AUTO_TEST_CASE() [87/95]

BOOST_AUTO_TEST_CASE ( testInterruptTblastnExitImmediately  )

◆ BOOST_AUTO_TEST_CASE() [88/95]

BOOST_AUTO_TEST_CASE ( testInterruptTblastxExitAtRandom  )

◆ BOOST_AUTO_TEST_CASE() [89/95]

BOOST_AUTO_TEST_CASE ( testInterruptTblastxExitImmediately  )

◆ BOOST_AUTO_TEST_CASE() [90/95]

BOOST_AUTO_TEST_CASE ( testInterruptTblastxExitOnTraceback  )

◆ BOOST_AUTO_TEST_CASE() [91/95]

BOOST_AUTO_TEST_CASE ( testMultiSeqSearchSymmetry  )

◆ BOOST_AUTO_TEST_CASE() [92/95]

BOOST_AUTO_TEST_CASE ( testOneSubjectResults2CSeqAlign  )

◆ BOOST_AUTO_TEST_CASE() [93/95]

BOOST_AUTO_TEST_CASE ( UnsupportedOption  )

◆ BOOST_AUTO_TEST_CASE() [94/95]

BOOST_AUTO_TEST_CASE ( WindowMaskerPathInitInvalid  )

Definition at line 2117 of file bl2seq_unit_test.cpp.

References kEmptyStr, and WindowMaskerPathInit().

◆ BOOST_AUTO_TEST_CASE() [95/95]

BOOST_AUTO_TEST_CASE ( WindowMaskerPathInitValid  )

◆ BOOST_AUTO_TEST_CASE_TIMEOUT()

BOOST_AUTO_TEST_CASE_TIMEOUT ( testInterruptBlastSetup  ,
 
)

◆ callback_counter()

Boolean callback_counter ( SBlastProgress progress_info)

This callback never interrupts the BLAST search, its only purpose is to count the number of times this is invoked for the given input.

Also to be used in CBl2SeqTest::testInterruptXExitAtRandom.

Definition at line 212 of file bl2seq_unit_test.cpp.

References FALSE, and SBlastProgress::user_data.

Referenced by BOOST_AUTO_TEST_CASE().

◆ do_not_interrupt()

Boolean do_not_interrupt ( SBlastProgress )

Returns false so that the processing never stops in spite of a callback function to interrupt the process is provided.

Definition at line 204 of file bl2seq_unit_test.cpp.

References FALSE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ interrupt_after3calls()

Boolean interrupt_after3calls ( SBlastProgress )

The interruption occurs after 3 invokations of this callback.

Definition at line 235 of file bl2seq_unit_test.cpp.

References FALSE, and TRUE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ interrupt_at_random()

Boolean interrupt_at_random ( SBlastProgress progress_info)

This callback interrupts the BLAST search after the callback has been executed the requested number of times in the pair's second member.

This is used in CBl2SeqTest::testInterruptXExitAtRandom.

Definition at line 222 of file bl2seq_unit_test.cpp.

References FALSE, TRUE, and SBlastProgress::user_data.

Referenced by BOOST_AUTO_TEST_CASE().

◆ interrupt_immediately()

Boolean interrupt_immediately ( SBlastProgress )

Returns true so that the processing stops upon the first invocation of this callback.

Definition at line 197 of file bl2seq_unit_test.cpp.

References TRUE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ interrupt_on_traceback()

Boolean interrupt_on_traceback ( SBlastProgress progress_info)

The interruption occurs after starting the traceback stage.

Definition at line 246 of file bl2seq_unit_test.cpp.

References eTracebackSearch, FALSE, SBlastProgress::stage, and TRUE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_MakePackedInt2()

CRef<CSeq_loc> s_MakePackedInt2 ( CRef< CSeq_id id,
vector< TSeqRange > &  range_vec 
)

Definition at line 84 of file bl2seq_unit_test.cpp.

References NON_CONST_ITERATE, and CSeq_loc::SetPacked_int().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_SetupWithMultipleQueriesAndSubjects()

static CRef<CBl2Seq> s_SetupWithMultipleQueriesAndSubjects ( bool  query_is_nucl,
bool  subj_is_nucl,
EProgram  program 
)
static

◆ testBlastHitCounts()

void testBlastHitCounts ( CBl2Seq blaster,
EBl2seqTest  test_id 
)

◆ testIntervalWholeAlignment()

static void testIntervalWholeAlignment ( TSeqAlignVector sav)
static

Definition at line 2653 of file bl2seq_unit_test.cpp.

References Begin(), eNa_strand_minus, and eNa_strand_plus.

Referenced by BOOST_AUTO_TEST_CASE().

◆ testRawCutoffs()

void testRawCutoffs ( CBl2Seq blaster,
EProgram  program,
EBl2seqTest  test_id 
)

◆ testResultAlignments()

void testResultAlignments ( size_t  num_queries,
size_t  num_subjects,
TSeqAlignVector  result_alnvec 
)

◆ testWholeIntervalAlignment()

static void testWholeIntervalAlignment ( TSeqAlignVector sav)
static

Definition at line 2679 of file bl2seq_unit_test.cpp.

References Begin(), eNa_strand_minus, and eNa_strand_plus.

Referenced by BOOST_AUTO_TEST_CASE().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )

◆ x_TestAlignmentQuerySubjStrandCombinations()

void x_TestAlignmentQuerySubjStrandCombinations ( TSeqAlignVector sav,
string  aligned_strands 
)

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 78 of file bl2seq_unit_test.cpp.

Modified on Wed Jul 24 17:18:48 2024 by modify_doxy.py rev. 669887