NCBI C++ ToolKit
Classes | Macros | Functions
pssmcreate_unit_test.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <corelib/ncbi_limits.hpp>
#include <serial/serial.hpp>
#include <serial/objistr.hpp>
#include <util/random_gen.hpp>
#include <util/math/matrix.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/scoremat/Pssm.hpp>
#include <objects/scoremat/PssmParameters.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <objects/scoremat/PssmFinalData.hpp>
#include <objects/scoremat/PssmIntermediateData.hpp>
#include <objects/scoremat/FormatRpsDbParameters.hpp>
#include <algo/blast/api/blast_aux.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/pssm_engine.hpp>
#include <algo/blast/api/pssm_input.hpp>
#include <algo/blast/api/psi_pssm_input.hpp>
#include <algo/blast/core/blast_setup.h>
#include <blast_objmgr_priv.hpp>
#include <blast_psi_priv.h>
#include <blast_posit.h>
#include "psiblast_aux_priv.hpp"
#include <algo/blast/api/blast_exception.hpp>
#include "blast_test_util.hpp"
#include "pssm_test_util.hpp"
#include <objmgr/util/sequence.hpp>
#include <util/tables/raw_scoremat.h>
#include <objects/seq/seqport_util.hpp>
#include "test_objmgr.hpp"
+ Include dependency graph for pssmcreate_unit_test.cpp:

Go to the source code of this file.

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Classes

class  CPssmInputFlankingGaps
 Mock object for the PSSM input data which returns multiple sequence alignment data which has flanking gaps. More...
 
class  CPssmInputGapsInQuery
 Mock object for the PSSM input data which returns a query sequence with a gap in it. More...
 
class  CPssmInputQueryLength0
 Mock object for the PSSM input data which returns a query sequence with a gap in it. More...
 
class  CNullPssmInput
 Mock object for the PSSM input data which returns NULLs for all its methods. More...
 
class  CPssmInputUnsupportedMatrix
 
class  CPssmInputTestData
 Mock object for the PSSM input data which can be configured to have different combinations of aligned sequences. More...
 

Macros

#define GAP_IN_ALIGNMENT   -1
 

Functions

 BOOST_AUTO_TEST_CASE (testFullPssmEngineRunWithDiagnosticsRequest)
 
 BOOST_AUTO_TEST_CASE (testSeqAlignToPsiBlastMultipleSequenceAlignment)
 
 BOOST_AUTO_TEST_CASE (testPurgeSequencesWithNull)
 Unit test the individual stages of the PSSM creation algorithm (core layer): 1. More...
 
 BOOST_AUTO_TEST_CASE (testPurgeSelfHit)
 
 BOOST_AUTO_TEST_CASE (testPurgeDuplicateHit)
 
 BOOST_AUTO_TEST_CASE (testPurgeNearIdenticalHits)
 
 BOOST_AUTO_TEST_CASE (testQueryAlignedWithInternalGaps)
 
 BOOST_AUTO_TEST_CASE (testMultiSeqAlignmentHasRegionsUnalignedToQuery)
 
 BOOST_AUTO_TEST_CASE (testQueryIsOnlyAlignedSequenceInMsa)
 test the case when only a segment of the query sequence is the only aligned sequence in the multiple sequence alignment. More...
 
 BOOST_AUTO_TEST_CASE (testRejectFlankingGaps)
 
 BOOST_AUTO_TEST_CASE (testRejectGapInQuery)
 
 BOOST_AUTO_TEST_CASE (testRejectQueryLength0)
 
 BOOST_AUTO_TEST_CASE (testRejectNullPssmInputData)
 
 BOOST_AUTO_TEST_CASE (testRejectNullsReturnedByPssmInput)
 
 BOOST_AUTO_TEST_CASE (testRejectUnsupportedMatrix)
 
 BOOST_AUTO_TEST_CASE (testPsiAlignmentDataCreation_TooMuchMemory)
 
 BOOST_AUTO_TEST_CASE (testPsiLowerCaseMatrix)
 

Macro Definition Documentation

◆ GAP_IN_ALIGNMENT

#define GAP_IN_ALIGNMENT   -1

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/17]

BOOST_AUTO_TEST_CASE ( testFullPssmEngineRunWithDiagnosticsRequest  )

◆ BOOST_AUTO_TEST_CASE() [2/17]

BOOST_AUTO_TEST_CASE ( testMultiSeqAlignmentHasRegionsUnalignedToQuery  )

◆ BOOST_AUTO_TEST_CASE() [3/17]

BOOST_AUTO_TEST_CASE ( testPsiAlignmentDataCreation_TooMuchMemory  )

Definition at line 1231 of file pssmcreate_unit_test.cpp.

References max(), NULL, and PSIMsaNew().

◆ BOOST_AUTO_TEST_CASE() [4/17]

BOOST_AUTO_TEST_CASE ( testPsiLowerCaseMatrix  )

◆ BOOST_AUTO_TEST_CASE() [5/17]

BOOST_AUTO_TEST_CASE ( testPurgeDuplicateHit  )

◆ BOOST_AUTO_TEST_CASE() [6/17]

BOOST_AUTO_TEST_CASE ( testPurgeNearIdenticalHits  )

◆ BOOST_AUTO_TEST_CASE() [7/17]

BOOST_AUTO_TEST_CASE ( testPurgeSelfHit  )

◆ BOOST_AUTO_TEST_CASE() [8/17]

BOOST_AUTO_TEST_CASE ( testPurgeSequencesWithNull  )

Unit test the individual stages of the PSSM creation algorithm (core layer): 1.

purged biased sequences

Definition at line 757 of file pssmcreate_unit_test.cpp.

References _PSIPurgeBiasedSegments(), NULL, and PSIERR_BADPARAM.

◆ BOOST_AUTO_TEST_CASE() [9/17]

BOOST_AUTO_TEST_CASE ( testQueryAlignedWithInternalGaps  )

◆ BOOST_AUTO_TEST_CASE() [10/17]

BOOST_AUTO_TEST_CASE ( testQueryIsOnlyAlignedSequenceInMsa  )

◆ BOOST_AUTO_TEST_CASE() [11/17]

BOOST_AUTO_TEST_CASE ( testRejectFlankingGaps  )

Definition at line 1196 of file pssmcreate_unit_test.cpp.

References CPssmEngine::Run().

◆ BOOST_AUTO_TEST_CASE() [12/17]

BOOST_AUTO_TEST_CASE ( testRejectGapInQuery  )

Definition at line 1202 of file pssmcreate_unit_test.cpp.

References CPssmEngine::Run().

◆ BOOST_AUTO_TEST_CASE() [13/17]

BOOST_AUTO_TEST_CASE ( testRejectNullPssmInputData  )

Definition at line 1213 of file pssmcreate_unit_test.cpp.

References NULL.

◆ BOOST_AUTO_TEST_CASE() [14/17]

BOOST_AUTO_TEST_CASE ( testRejectNullsReturnedByPssmInput  )

Definition at line 1218 of file pssmcreate_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [15/17]

BOOST_AUTO_TEST_CASE ( testRejectQueryLength0  )

Definition at line 1208 of file pssmcreate_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [16/17]

BOOST_AUTO_TEST_CASE ( testRejectUnsupportedMatrix  )

Definition at line 1223 of file pssmcreate_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [17/17]

BOOST_AUTO_TEST_CASE ( testSeqAlignToPsiBlastMultipleSequenceAlignment  )
Modified on Fri Feb 23 11:42:23 2024 by modify_doxy.py rev. 669887