NCBI C++ ToolKit
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pssmcreate_cdd_unit_test.cpp File Reference

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  )

◆ BOOST_AUTO_TEST_CASE() [2/13]

BOOST_AUTO_TEST_CASE ( TestCreatePssmFromMultipleCds  )

◆ BOOST_AUTO_TEST_CASE() [3/13]

BOOST_AUTO_TEST_CASE ( TestCreatePssmFromNoCds  )

◆ BOOST_AUTO_TEST_CASE() [4/13]

BOOST_AUTO_TEST_CASE ( TestCreatePssmFromSingleCd  )

◆ BOOST_AUTO_TEST_CASE() [5/13]

BOOST_AUTO_TEST_CASE ( TestDuplicateCdHits  )

◆ BOOST_AUTO_TEST_CASE() [6/13]

BOOST_AUTO_TEST_CASE ( TestFullPssmEngineRunWithDiagnosticsRequest  )

◆ 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  )

◆ s_TestCreatePssmFromFreqs()

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

Variable Documentation

◆ kQueryId

const string kQueryId = "gi|129295"
static

Query id used for tests.

Definition at line 81 of file pssmcreate_cdd_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CPssmCddInputTest::CreatePssmInput().

◆ kSubjectId

const string kSubjectId = "gnl|CDD|29117"
static

Domain subject id used for tests (present in test CDD)

Definition at line 84 of file pssmcreate_cdd_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), CPssmCddInputTest::x_CreateDuplicateNonOverlappingHit(), and CPssmCddInputTest::x_CreateDuplicateOverlappingHit().

Modified on Wed May 29 18:39:28 2024 by modify_doxy.py rev. 669887