Unit test module for creation of PSSMs from multiple alignments of conserved domains. More...

#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <serial/serial.hpp>
#include <serial/objistr.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/Bioseq.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 <algo/blast/api/pssm_engine.hpp>
#include <algo/blast/api/pssm_input.hpp>
#include <algo/blast/api/cdd_pssm_input.hpp>
#include <algo/blast/api/rps_aux.hpp>
#include <blast_objmgr_priv.hpp>
#include <blast_psi_priv.h>
#include "psiblast_aux_priv.hpp"
#include "blast_test_util.hpp"
#include "pssm_test_util.hpp"
#include "test_objmgr.hpp"

Include dependency graph for pssmcreate_cdd_unit_test.cpp:

Go to the source code of this file.

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Classes
class	CPssmCddInputTest
	Class for testing methods of CCddInputData class. More...

class	CPssmInputWithNoCDs
	Simple PSSM computation strategy with one CD. More...

class	CPssmInputWithSingleCD
	Simple PSSM computation strategy with one CD. More...

class	CPssmInputWithTwoCDs
	Simple PSSM computation strategy with two CDs. More...

class	CPssmInputWithGapsInQuery
	PSSM computation strategy with gaps in query. More...

class	CPssmInputWithNegativeFreqs
	PSSM computation strategy with domains with negative residue frequencies. More...

class	CPssmInputWithUnnormalizedFreqs
	PSSM computation strategy with domains with frequencies that do not sum to 1. More...

class	CPssmInputWithZeroObservations
	PSSM computation strategy with domains with zero observations. More...

Macros
#define	BLAST_SECONDARY_SOURCE 1

Functions
static void	s_TestCreatePssmFromFreqs (const PSICdMsa cd_msa, CBlastScoreBlk &sbp, const PSIBlastOptions opts, AutoPtr< _PSISequenceWeights > &seq_weights)

	BOOST_AUTO_TEST_CASE (TestCreatePssmFromSingleCd)

	BOOST_AUTO_TEST_CASE (TestCreatePssmFromMultipleCds)

	BOOST_AUTO_TEST_CASE (TestCreatePssmFromNoCds)

	BOOST_AUTO_TEST_CASE (TestRejectGapsInQuery)

	BOOST_AUTO_TEST_CASE (TestRejectDomainsWithNegativeFreqs)

	BOOST_AUTO_TEST_CASE (TestRejectDomainsWithUnnormalizedFreqs)

	BOOST_AUTO_TEST_CASE (TestRejectDomainsWithZeroObservations)

	BOOST_AUTO_TEST_CASE (TestRejectNullInput)

	BOOST_AUTO_TEST_CASE (TestConvertSeqalignToCdMsa)

	BOOST_AUTO_TEST_CASE (TestDuplicateCdHits)

	BOOST_AUTO_TEST_CASE (TestFullPssmEngineRunWithDiagnosticsRequest)

	BOOST_AUTO_TEST_CASE (TestInternalGapsInSubject)

	BOOST_AUTO_TEST_CASE (TestNoDomainHits)

Variables
static const string	kQueryId = "gi\|129295"
	Query id used for tests. More...

static const string	kSubjectId = "gnl\|CDD\|29117"
	Domain subject id used for tests (present in test CDD) More...

Detailed Description

Unit test module for creation of PSSMs from multiple alignments of conserved domains.

Definition in file pssmcreate_cdd_unit_test.cpp.

Macro Definition Documentation

◆ BLAST_SECONDARY_SOURCE

#define BLAST_SECONDARY_SOURCE 1

Definition at line 36 of file pssmcreate_cdd_unit_test.cpp.

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/13]

BOOST_AUTO_TEST_CASE ( TestConvertSeqalignToCdMsa )

Definition at line 507 of file pssmcreate_cdd_unit_test.cpp.

References abs, PSICdMsaCell::data, SBlastSequence::data, data, PSICdMsa::dimensions, eBlastEncodingProtein, CSeqDB::eProtein, eSerial_AsnText, CBlastRPSInfo::fDeltaBlast, AutoPtr< X, Del >::get(), CSeq_align_set_Base::Get(), CPssmCddInputTest::GetAlphabetSize(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CPssmCddInputTest::GetMsaSize(), CDense_seg_Base::GetNumseg(), CPssmCddInputTest::GetProfilesDataScale(), CDense_seg::GetSeq_id(), GetSequence(), CDense_seg_Base::GetStarts(), CPssmCddInputTest::GetSubjectMsaIndex(), i, in(), CTestObjMgr::Instance(), int, PSICdMsaCell::is_aligned, ITERATE, kAlphabetSize, kScale, SBlastSequence::length, PSICdMsa::msa, BlastRPSProfileHeader::num_profiles, PSIMsaDimensions::num_seqs, CObjectIStream::Open(), PSIBlastOptionsNew(), PSICdMsa::query, PSIMsaDimensions::query_length, BlastRPSProfileHeader::start_offsets, subject, and val.

◆ BOOST_AUTO_TEST_CASE() [2/13]

BOOST_AUTO_TEST_CASE ( TestCreatePssmFromMultipleCds )

◆ BOOST_AUTO_TEST_CASE() [3/13]

BOOST_AUTO_TEST_CASE ( TestCreatePssmFromNoCds )

Definition at line 376 of file pssmcreate_cdd_unit_test.cpp.

References _PSIComputeFrequenciesFromCDs(), _PSISequenceWeightsNew(), PSICdMsa::dimensions, CBlastScoreBlk::Get(), AutoPtr< X, Del >::get(), CPssmInputWithNoCDs::GetData(), CPssmInputWithNoCDs::GetOptions(), CPssmInputWithNoCDs::GetQuery(), CPssmInputWithNoCDs::GetQueryLength(), InitializeBlastScoreBlk(), CBlastScoreBlk::Reset(), s_TestCreatePssmFromFreqs(), and CPssmCreateTestFixture::x_GuardProteinQuery().

◆ BOOST_AUTO_TEST_CASE() [4/13]

BOOST_AUTO_TEST_CASE ( TestCreatePssmFromSingleCd )

◆ BOOST_AUTO_TEST_CASE() [5/13]

BOOST_AUTO_TEST_CASE ( TestDuplicateCdHits )

Definition at line 729 of file pssmcreate_cdd_unit_test.cpp.

References CPssmCddInputTest::CreatePssmInput(), CPssmCddInputTest::eDuplicateNonOverlappingHit, CPssmCddInputTest::eDuplicateOverlappingHit, CPssmCddInputTest::GetNumHits(), and CPssmCddInputTest::RemoveMultipleCdHits().

◆ BOOST_AUTO_TEST_CASE() [6/13]

BOOST_AUTO_TEST_CASE ( TestFullPssmEngineRunWithDiagnosticsRequest )

Definition at line 771 of file pssmcreate_cdd_unit_test.cpp.

References BLASTAA_SIZE, SBlastSequence::data, data, eBlastEncodingProtein, eSerial_AsnText, PSIDiagnosticsRequest::frequency_ratios, AutoPtr< X, Del >::get(), CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CPssm_Base::GetFinalData(), CPssmIntermediateData_Base::GetFreqRatios(), CPssm_Base::GetIntermediateData(), CBioseq::GetLength(), CPssmIntermediateData_Base::GetNumIndeptObsr(), CPssmWithParameters_Base::GetPssm(), CPssmFinalData_Base::GetScores(), GetSequence(), CPssmIntermediateData_Base::GetWeightedResFreqsPerPos(), in(), PSIDiagnosticsRequest::independent_observations, PSIDiagnosticsRequest::information_content, CTestObjMgr::Instance(), CBioseq_Base::IsSetDescr(), ITERATE, kTitle, SBlastSequence::length, CObjectIStream::Open(), PSIBlastOptionsNew(), and PSIDiagnosticsRequest::weighted_residue_frequencies.

◆ BOOST_AUTO_TEST_CASE() [7/13]

BOOST_AUTO_TEST_CASE ( TestInternalGapsInSubject )

◆ BOOST_AUTO_TEST_CASE() [8/13]

BOOST_AUTO_TEST_CASE ( TestNoDomainHits )

◆ BOOST_AUTO_TEST_CASE() [9/13]

BOOST_AUTO_TEST_CASE ( TestRejectDomainsWithNegativeFreqs )

Definition at line 416 of file pssmcreate_cdd_unit_test.cpp.

References CPssmEngine::Run().

◆ BOOST_AUTO_TEST_CASE() [10/13]

BOOST_AUTO_TEST_CASE ( TestRejectDomainsWithUnnormalizedFreqs )

Definition at line 424 of file pssmcreate_cdd_unit_test.cpp.

References CPssmEngine::Run().

◆ BOOST_AUTO_TEST_CASE() [11/13]

BOOST_AUTO_TEST_CASE ( TestRejectDomainsWithZeroObservations )

Definition at line 432 of file pssmcreate_cdd_unit_test.cpp.

References CPssmEngine::Run().

◆ BOOST_AUTO_TEST_CASE() [12/13]

BOOST_AUTO_TEST_CASE ( TestRejectGapsInQuery )

Definition at line 407 of file pssmcreate_cdd_unit_test.cpp.

References CPssmEngine::Run().

◆ BOOST_AUTO_TEST_CASE() [13/13]

BOOST_AUTO_TEST_CASE ( TestRejectNullInput )

Definition at line 441 of file pssmcreate_cdd_unit_test.cpp.

References _PSIComputeFreqRatiosFromCDs(), _PSIComputeFrequenciesFromCDs(), _PSIInternalPssmDataNew(), _PSISequenceWeightsNew(), BlastScoreBlk::alphabet_size, PSICdMsa::dimensions, CBlastScoreBlk::Get(), AutoPtr< X, Del >::get(), CPssmInputWithNoCDs::GetData(), CPssmInputWithNoCDs::GetOptions(), CPssmInputWithNoCDs::GetQuery(), CPssmInputWithNoCDs::GetQueryLength(), InitializeBlastScoreBlk(), NULL, PSIMsaDimensions::query_length, CBlastScoreBlk::Reset(), and CPssmCreateTestFixture::x_GuardProteinQuery().

◆ s_TestCreatePssmFromFreqs()

void s_TestCreatePssmFromFreqs	(	const PSICdMsa *	cd_msa,
		CBlastScoreBlk &	sbp,
		const PSIBlastOptions *	opts,
		AutoPtr< _PSISequenceWeights > &	seq_weights
	)