NCBI C++ ToolKit
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CSequenceDataTester Class Reference

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Public Member Functions

 CSequenceDataTester (CRef< IQueryFactory > query_factory, TGi gi)
 
 CSequenceDataTester (CRef< IQueryFactory > query_factory, const vector< TGi > &gis)
 
 CSequenceDataTester (CRef< IQueryFactory > query_factory, const IRemoteQueryData::TSeqLocs &seqlocs)
 
void operator() (void)
 

Private Member Functions

void x_Init (const IRemoteQueryData::TSeqLocs *seqlocs=0)
 
bool x_IsProtein ()
 
ENa_strand x_GetStrand (int index)
 
void x_TestSingleSequence_Local (int index)
 
void x_TestSingleSequence_Remote (int index)
 
void x_TestSingleProtein_Local (int index, const BlastQueryInfo *qinfo, const BLAST_SequenceBlk *seqblk)
 
void x_TestSingleNucleotide_Local (int index, const BlastQueryInfo *qinfo, const BLAST_SequenceBlk *seqblk)
 
void x_TestSingleTranslatedNucl_Local (int index, const BlastQueryInfo *qinfo, const BLAST_SequenceBlk *seqblk)
 
void x_TestSingleProtein_Remote (const CSeq_id &id, const CSeq_inst &seq_inst)
 
void x_TestSingleNucleotide_Remote (const CSeq_id &id, const CSeq_inst &seq_inst)
 
void x_TestLocalStrand (const CSeq_id &id, int ctx_index, ENa_strand strand, const BlastQueryInfo *qinfo, const BLAST_SequenceBlk *seqblk)
 
void x_CompareSequenceData (CSeqVector &sv, const Uint1 *sequence, const string &strand="")
 

Private Attributes

CRef< IQueryFactory > m_QueryFactory
 
vector< TGi > m_Gis
 
vector< ENa_strand > m_Strands
 
CConstRef< CBlastOptions > m_Options
 
CRef< CScope > m_Scope
 

Detailed Description

Definition at line 67 of file querydata_unit_test.cpp.

Constructor & Destructor Documentation

◆ CSequenceDataTester() [1/3]

CSequenceDataTester::CSequenceDataTester ( CRef< IQueryFactory >  query_factory,
TGi  gi 
)

Definition at line 117 of file querydata_unit_test.cpp.

References x_Init().

◆ CSequenceDataTester() [2/3]

CSequenceDataTester::CSequenceDataTester ( CRef< IQueryFactory >  query_factory,
const vector< TGi > &  gis 
)

Definition at line 124 of file querydata_unit_test.cpp.

References x_Init().

◆ CSequenceDataTester() [3/3]

CSequenceDataTester::CSequenceDataTester ( CRef< IQueryFactory >  query_factory,
const IRemoteQueryData::TSeqLocs &  seqlocs 
)

Definition at line 132 of file querydata_unit_test.cpp.

References x_Init().

Member Function Documentation

◆ operator()()

void CSequenceDataTester::operator() ( void  )

Definition at line 214 of file querydata_unit_test.cpp.

References i, m_Gis, x_TestSingleSequence_Local(), and x_TestSingleSequence_Remote().

◆ x_CompareSequenceData()

void CSequenceDataTester::x_CompareSequenceData ( CSeqVector &  sv,
const Uint1 *  sequence,
const string &  strand = "" 
)
private

Definition at line 280 of file querydata_unit_test.cpp.

References CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbistdaa, i, NStr::IntToString(), CSeqVector::IsNucleotide(), CSeqVector::IsProtein(), msg(), NCBI4NA_TO_BLASTNA, CSeqVector::SetCoding(), CSeqVector::size(), and x_IsProtein().

Referenced by x_TestLocalStrand(), and x_TestSingleProtein_Local().

◆ x_GetStrand()

ENa_strand CSequenceDataTester::x_GetStrand ( int  index)
inlineprivate

Definition at line 208 of file querydata_unit_test.cpp.

References m_Strands.

Referenced by x_TestSingleNucleotide_Local().

◆ x_Init()

void CSequenceDataTester::x_Init ( const IRemoteQueryData::TSeqLocs *  seqlocs = 0)
private

Definition at line 141 of file querydata_unit_test.cpp.

References CBlastOptionsFactory::Create(), eBlastn, eBlastp, eNa_strand_both, eNa_strand_unknown, CBioseq_Handle::GetBioseqCore(), CSimpleOM::GetBioseqHandle(), GetGiForAccession(), GetId(), CBioseq_Base::GetInst(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetStrandOption(), CSeq_inst::IsAa(), ITERATE, m_Gis, m_Options, m_Scope, m_Strands, CSimpleOM::NewScope(), prog, CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), x_IsProtein(), and ZERO_GI.

Referenced by CSequenceDataTester(), and x_IsProtein().

◆ x_IsProtein()

bool CSequenceDataTester::x_IsProtein ( )
private

Definition at line 199 of file querydata_unit_test.cpp.

References Blast_QueryIsProtein(), CBlastOptions::GetProgramType(), m_Options, and x_Init().

Referenced by x_CompareSequenceData(), x_Init(), x_TestSingleSequence_Local(), and x_TestSingleSequence_Remote().

◆ x_TestLocalStrand()

void CSequenceDataTester::x_TestLocalStrand ( const CSeq_id &  id,
int  ctx_index,
ENa_strand  strand,
const BlastQueryInfo *  qinfo,
const BLAST_SequenceBlk *  seqblk 
)
private

Definition at line 248 of file querydata_unit_test.cpp.

References BlastQueryInfo::contexts, eNa_strand_minus, eNa_strand_plus, GetLength(), CSimpleOM::GetSeqVector(), m_Scope, BlastContextInfo::query_length, BlastContextInfo::query_offset, BLAST_SequenceBlk::sequence, and x_CompareSequenceData().

Referenced by x_TestSingleNucleotide_Local().

◆ x_TestSingleNucleotide_Local()

void CSequenceDataTester::x_TestSingleNucleotide_Local ( int  index,
const BlastQueryInfo *  qinfo,
const BLAST_SequenceBlk *  seqblk 
)
private

Definition at line 223 of file querydata_unit_test.cpp.

References CSeq_id_Base::e_Gi, eNa_strand_both, eNa_strand_minus, eNa_strand_plus, m_Gis, NCBI_CURRENT_FUNCTION, x_GetStrand(), and x_TestLocalStrand().

Referenced by x_TestSingleSequence_Local().

◆ x_TestSingleNucleotide_Remote()

void CSequenceDataTester::x_TestSingleNucleotide_Remote ( const CSeq_id &  id,
const CSeq_inst &  seq_inst 
)
private

Definition at line 449 of file querydata_unit_test.cpp.

References CSeqportUtil::Convert(), CSeq_data_Base::e_Ncbi4na, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetNcbi4na(), CSeq_inst_Base::GetSeq_data(), CSimpleOM::GetSeqVector(), i, int, NStr::IntToString(), CSeq_inst::IsAa(), CSeq_data_Base::IsNcbi4na(), CSeqVector::IsProtein(), CSeqVector::SetCoding(), and CSeqVector::size().

Referenced by x_TestSingleSequence_Remote().

◆ x_TestSingleProtein_Local()

void CSequenceDataTester::x_TestSingleProtein_Local ( int  index,
const BlastQueryInfo *  qinfo,
const BLAST_SequenceBlk *  seqblk 
)
private

Definition at line 310 of file querydata_unit_test.cpp.

References BlastQueryInfo::contexts, CSeq_id_Base::e_Gi, BlastQueryInfo::first_context, GetLength(), CSimpleOM::GetSeqVector(), m_Gis, m_Scope, BlastContextInfo::query_length, BlastContextInfo::query_offset, BLAST_SequenceBlk::sequence, and x_CompareSequenceData().

Referenced by x_TestSingleSequence_Local().

◆ x_TestSingleProtein_Remote()

void CSequenceDataTester::x_TestSingleProtein_Remote ( const CSeq_id &  id,
const CSeq_inst &  seq_inst 
)
private

Definition at line 428 of file querydata_unit_test.cpp.

References CSeqportUtil::Convert(), CSeq_data_Base::e_Ncbistdaa, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetNcbistdaa(), CSeq_inst_Base::GetSeq_data(), CSimpleOM::GetSeqVector(), i, NStr::IntToString(), CSeq_inst::IsAa(), CSeq_data_Base::IsNcbistdaa(), CSeqVector::IsProtein(), CSeqVector::SetCoding(), and CSeqVector::size().

Referenced by x_TestSingleSequence_Remote().

◆ x_TestSingleSequence_Local()

void CSequenceDataTester::x_TestSingleSequence_Local ( int  index)
private

Definition at line 330 of file querydata_unit_test.cpp.

References CRef< C, Locker >::GetNonNullPointer(), ILocalQueryData::GetQueryInfo(), ILocalQueryData::GetQueryMessages(), ILocalQueryData::GetSequenceBlk(), ITERATE, m_Gis, m_Options, m_QueryFactory, IQueryFactory::MakeLocalQueryData(), NCBI_THROW, CRef< C, Locker >::NotEmpty(), NULL, BlastQueryInfo::num_queries, x_IsProtein(), x_TestSingleNucleotide_Local(), and x_TestSingleProtein_Local().

Referenced by operator()().

◆ x_TestSingleSequence_Remote()

void CSequenceDataTester::x_TestSingleSequence_Remote ( int  index)
private

Definition at line 366 of file querydata_unit_test.cpp.

References CSeq_id::AsFastaString(), ConstBegin(), CSeq_id_Base::e_Gi, CSeq_inst_Base::eRepr_raw, IRemoteQueryData::GetBioseqSet(), GetLength(), CSeq_inst_Base::GetLength(), CRef< C, Locker >::GetNonNullPointer(), CSeq_inst_Base::GetRepr(), IRemoteQueryData::GetSeqLocs(), i, NStr::IntToString(), CSeq_inst::IsAa(), m_Gis, m_QueryFactory, m_Scope, IQueryFactory::MakeRemoteQueryData(), CRef< C, Locker >::NotEmpty(), NPOS, NULL, x_IsProtein(), x_TestSingleNucleotide_Remote(), and x_TestSingleProtein_Remote().

Referenced by operator()().

◆ x_TestSingleTranslatedNucl_Local()

void CSequenceDataTester::x_TestSingleTranslatedNucl_Local ( int  index,
const BlastQueryInfo *  qinfo,
const BLAST_SequenceBlk *  seqblk 
)
private

Definition at line 270 of file querydata_unit_test.cpp.

References msg().

Member Data Documentation

◆ m_Gis

vector<TGi> CSequenceDataTester::m_Gis
private

Definition at line 83 of file querydata_unit_test.cpp.

Referenced by operator()(), x_Init(), x_TestSingleNucleotide_Local(), x_TestSingleProtein_Local(), x_TestSingleSequence_Local(), and x_TestSingleSequence_Remote().

◆ m_Options

CConstRef<CBlastOptions> CSequenceDataTester::m_Options
private

Definition at line 85 of file querydata_unit_test.cpp.

Referenced by x_Init(), x_IsProtein(), and x_TestSingleSequence_Local().

◆ m_QueryFactory

CRef<IQueryFactory> CSequenceDataTester::m_QueryFactory
private

Definition at line 82 of file querydata_unit_test.cpp.

Referenced by x_TestSingleSequence_Local(), and x_TestSingleSequence_Remote().

◆ m_Scope

CRef<CScope> CSequenceDataTester::m_Scope
private

Definition at line 86 of file querydata_unit_test.cpp.

Referenced by x_Init(), x_TestLocalStrand(), x_TestSingleProtein_Local(), and x_TestSingleSequence_Remote().

◆ m_Strands

vector<ENa_strand> CSequenceDataTester::m_Strands
private

Definition at line 84 of file querydata_unit_test.cpp.

Referenced by x_GetStrand(), and x_Init().

The documentation for this class was generated from the following file:
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Modified on Wed Sep 04 15:06:15 2024 by modify_doxy.py rev. 669887