#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <serial/iterator.hpp>
#include <algo/blast/api/psiblast.hpp>
#include <algo/blast/api/uniform_search.hpp>
#include <algo/blast/api/local_db_adapter.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/blastinput/blast_scope_src.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <algo/blast/api/pssm_engine.hpp>
#include <algo/blast/api/psi_pssm_input.hpp>
#include <objects/scoremat/Pssm.hpp>
#include <objects/scoremat/PssmFinalData.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <objects/scoremat/PssmIntermediateData.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include "psiblast_aux_priv.hpp"
#include "blast_test_util.hpp"
#include "seqalign_cmp.hpp"
#include "seqalign_set_convert.hpp"
#include <algo/blast/api/psiblast_iteration.hpp>
#include "bioseq_extract_data_priv.hpp"
#include "blast_objmgr_priv.hpp"

Include dependency graph for psiblast_unit_test.cpp:

Go to the SVN repository for this file.

Classes
struct	CPsiBlastTestFixture

Macros
#define	NCBI_TEST_APPLICATION

#define	STATIC_ARRAY_SIZE(array) (sizeof(array)/sizeof(*array))
	Calculate the size of a static array. More...

Functions
	BOOST_AUTO_TEST_CASE (TestSingleIteration_ProteinAsQuery_NoCBS)

	BOOST_AUTO_TEST_CASE (TestSingleIteration_ProteinAsQuery_CBS)

	BOOST_AUTO_TEST_CASE (TestSingleIteration_ProteinAsQuery_CBSConditional)

	BOOST_AUTO_TEST_CASE (TestSingleIteration_ProteinAsQuery_CBSUniversal)

	BOOST_AUTO_TEST_CASE (TestMultipleIterationsAndConvergence_ProteinAsQuery_NoCBS)

	BOOST_AUTO_TEST_CASE (TestSingleIteration_PssmAsQuery_NoCBS)

	BOOST_AUTO_TEST_CASE (TestSingleIteration_PssmAsQuery_CBS)

	BOOST_AUTO_TEST_CASE (TestMultipleIterationsAndConvergence_PssmAsQuery_NoCBS)

	BOOST_AUTO_TEST_CASE (TestMultipleIterationsAndConvergence_PssmAsQuery_CBS)

	BOOST_AUTO_TEST_CASE (TestMultipleQueries)

	BOOST_AUTO_TEST_CASE (TestNullQuery)

	BOOST_AUTO_TEST_CASE (TestFrequencyRatiosWithAllZerosInPssm)

	BOOST_AUTO_TEST_CASE (TestNullPssm)

	BOOST_AUTO_TEST_CASE (TestSetNullPssm)

	BOOST_AUTO_TEST_CASE (TestNonExistantDb)

	BOOST_AUTO_TEST_CASE (TestNullOptions)

Macro Definition Documentation

◆ NCBI_TEST_APPLICATION

#define NCBI_TEST_APPLICATION

Definition at line 33 of file psiblast_unit_test.cpp.

◆ STATIC_ARRAY_SIZE

#define STATIC_ARRAY_SIZE ( array ) (sizeof(array)/sizeof(*array))

Calculate the size of a static array.

Definition at line 73 of file psiblast_unit_test.cpp.

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/16]

BOOST_AUTO_TEST_CASE ( TestFrequencyRatiosWithAllZerosInPssm )

Definition at line 1183 of file psiblast_unit_test.cpp.

References eBlastSevWarning, ITERATE, NON_CONST_ITERATE, r(), and CPsiBlast::Run().

◆ BOOST_AUTO_TEST_CASE() [2/16]

BOOST_AUTO_TEST_CASE ( TestMultipleIterationsAndConvergence_ProteinAsQuery_NoCBS )

Definition at line 557 of file psiblast_unit_test.cpp.

References CPsiBlastIterationState::Advance(), ctll::empty(), eNoCompositionBasedStats, CSeq_align_set_Base::Get(), CPsiBlastIterationState::GetIterationNumber(), CPsiBlastIterationState::GetSeqIds(), NStr::IntToString(), results, CPsiBlast::Run(), CPsiBlast::SetPssm(), set< Key, Compare >::size(), and NStr::SizetToString().

◆ BOOST_AUTO_TEST_CASE() [3/16]

BOOST_AUTO_TEST_CASE ( TestMultipleIterationsAndConvergence_PssmAsQuery_CBS )

Definition at line 1124 of file psiblast_unit_test.cpp.

References CPsiBlastIterationState::Advance(), eCompositionBasedStats, ctll::empty(), CPsiBlastIterationState::GetIterationNumber(), CPsiBlastIterationState::GetSeqIds(), NStr::IntToString(), CConstRef< C, Locker >::NotEmpty(), query, results, CPsiBlast::Run(), CPsiBlast::SetPssm(), set< Key, Compare >::size(), and NStr::SizetToString().

◆ BOOST_AUTO_TEST_CASE() [4/16]

BOOST_AUTO_TEST_CASE ( TestMultipleIterationsAndConvergence_PssmAsQuery_NoCBS )

Definition at line 1079 of file psiblast_unit_test.cpp.

References CPsiBlastIterationState::Advance(), ctll::empty(), eNoCompositionBasedStats, CPsiBlastIterationState::GetIterationNumber(), CPsiBlastIterationState::GetSeqIds(), NStr::IntToString(), query, results, CPsiBlast::Run(), CPsiBlast::SetPssm(), set< Key, Compare >::size(), and NStr::SizetToString().

◆ BOOST_AUTO_TEST_CASE() [5/16]

BOOST_AUTO_TEST_CASE ( TestMultipleQueries )

Definition at line 1169 of file psiblast_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [6/16]

BOOST_AUTO_TEST_CASE ( TestNonExistantDb )

Definition at line 1221 of file psiblast_unit_test.cpp.

References CPsiBlast::Run().

◆ BOOST_AUTO_TEST_CASE() [7/16]

BOOST_AUTO_TEST_CASE ( TestNullOptions )

Definition at line 1228 of file psiblast_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [8/16]

BOOST_AUTO_TEST_CASE ( TestNullPssm )

Definition at line 1207 of file psiblast_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [9/16]

BOOST_AUTO_TEST_CASE ( TestNullQuery )

Definition at line 1176 of file psiblast_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [10/16]

BOOST_AUTO_TEST_CASE ( TestSetNullPssm )

Definition at line 1214 of file psiblast_unit_test.cpp.

References CPsiBlast::SetPssm().

◆ BOOST_AUTO_TEST_CASE() [11/16]

BOOST_AUTO_TEST_CASE ( TestSingleIteration_ProteinAsQuery_CBS )

Definition at line 292 of file psiblast_unit_test.cpp.

References eCompositionBasedStats, ctll::empty(), results, CPsiBlast::Run(), and SeqAlignSetConvert().

◆ BOOST_AUTO_TEST_CASE() [12/16]

BOOST_AUTO_TEST_CASE ( TestSingleIteration_ProteinAsQuery_CBSConditional )

Definition at line 376 of file psiblast_unit_test.cpp.

References copy(), eCompositionMatrixAdjust, ctll::empty(), results, CPsiBlast::Run(), SeqAlignSetConvert(), and STATIC_ARRAY_SIZE.

◆ BOOST_AUTO_TEST_CASE() [13/16]

BOOST_AUTO_TEST_CASE ( TestSingleIteration_ProteinAsQuery_CBSUniversal )

Definition at line 469 of file psiblast_unit_test.cpp.

References copy(), eCompoForceFullMatrixAdjust, ctll::empty(), results, CPsiBlast::Run(), SeqAlignSetConvert(), and STATIC_ARRAY_SIZE.

◆ BOOST_AUTO_TEST_CASE() [14/16]

BOOST_AUTO_TEST_CASE ( TestSingleIteration_ProteinAsQuery_NoCBS )

Definition at line 205 of file psiblast_unit_test.cpp.

References copy(), ctll::empty(), eNoCompositionBasedStats, results, CPsiBlast::Run(), SeqAlignSetConvert(), and STATIC_ARRAY_SIZE.

◆ BOOST_AUTO_TEST_CASE() [15/16]

BOOST_AUTO_TEST_CASE ( TestSingleIteration_PssmAsQuery_CBS )

Definition at line 720 of file psiblast_unit_test.cpp.

References copy(), eCompositionBasedStats, ctll::empty(), results, CPsiBlast::Run(), SeqAlignSetConvert(), and STATIC_ARRAY_SIZE.

◆ BOOST_AUTO_TEST_CASE() [16/16]

BOOST_AUTO_TEST_CASE ( TestSingleIteration_PssmAsQuery_NoCBS )

Definition at line 601 of file psiblast_unit_test.cpp.