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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCSequenceDataTester.html below:

NCBI C++ ToolKit: CSequenceDataTester Class Reference

Search Toolkit Book for CSequenceDataTester

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="")

Definition at line 67 of file querydata_unit_test.cpp.

◆ CSequenceDataTester() [1/3] ◆ CSequenceDataTester() [2/3] ◆ CSequenceDataTester() [3/3] ◆ operator()() void CSequenceDataTester::operator() ( void ) ◆ x_CompareSequenceData()

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() ◆ x_Init()

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 ◆ x_TestLocalStrand() ◆ x_TestSingleNucleotide_Local() ◆ x_TestSingleNucleotide_Remote()

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()

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()

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() ◆ m_Gis vector<TGi> CSequenceDataTester::m_Gis private ◆ m_Options ◆ m_QueryFactory ◆ m_Scope ◆ m_Strands

The documentation for this class was generated from the following file:

src/algo/blast/unit_tests/api/querydata_unit_test.cpp

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