Definition at line 230 of file seq_vector.hpp.
◆ EFlagsSegment type flags.
Enumerator fFindData fFindGap fFindLeafRef fFindInnerRef fFindExactLevel fIgnoreUnresolved fByFeaturePolicy fBySequenceClass fFindRef fFindAny fFindAnyLeaf fDefaultFlagsDefinition at line 128 of file seq_map.hpp.
◆ ESegmentType Enumerator eSeqGapgap
eSeqDatareal sequence data
eSeqSubMapsub seqmap
eSeqRefreference to Bioseq
eSeqEnd eSeqChunk eSeqLiteralused only in m_ObjType for gap segments
Definition at line 96 of file seq_map.hpp.
◆ begin() [1/2] ◆ Begin() ◆ begin() [2/2]Definition at line 298 of file seq_vector.hpp.
References CSeqVector::CSeqVector_CI.
Referenced by CSplignFormatter::AsAlignmentText(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CChain::CollectTrustedmRNAsProts(), CAnnotCompare::CompareFeats(), Does3primerAbutGap(), Does5primerAbutGap(), ExtendCDSToStopCodon(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), variation::FindSSRLoc(), CInternalStopFinder::FindStartStopRanges(), CInternalStopFinder::GetCDSNucleotideSequence(), CExtendCDSToStop::GetCommand(), CBlastSeqVectorOM::GetCompressedPlusStrand(), CPostProcessUtils::GetLiteralAtLoc(), s_GetPolyA_genomic_priming(), CSeqTranslator::TranslateToProtein(), variation_ref::CHgvsParser::CContext::Validate(), CAgpFastaComparator::CTmpSeqVecStorage::WriteData(), CGapAnalysis::x_AddGapsFromBases(), CFeatureItem::x_AddQualsProt(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CFeaturePropagator::x_ExtendToStopCodon(), CVariationUtilities::x_GetAlleleFromLoc(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), variation::CVariationUtil::x_InferNAfromAA(), variation_ref::CHgvsParser::x_LocToSeqStr(), variation::CHgvsParser::x_LocToSeqStr(), variation_ref::CVariationUtil::x_ProtToPrecursor(), and CValidError_graph::x_ValidateGraphValues().
◆ BeginResolved() [1/2] ◆ BeginResolved() [2/2] ◆ CanGetRange() [1/2] ◆ CanGetRange() [2/2] ◆ CanResolveRange() [1/2]Definition at line 986 of file seq_map.cpp.
References _ASSERT, SSeqMapSelector::AddUsedTSE(), ConstRef(), CSeqMap::eSeqRef, CSeqMap::fFindAnyLeaf, Get(), AutoPtr< X, Del >::get(), CScope::GetBioseqHandles(), CDataLoader::GetChunks(), CSeqMap::GetLength(), CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefSeqid(), CSeqMap_CI::GetType(), i, kInvalidSeqPos, SSeqMapSelector::m_Length, SSeqMapSelector::m_LinkUsedTSE, SSeqMapSelector::m_MaxResolveCount, SSeqMapSelector::m_Position, CSeqMap_CI::m_Selector, SSeqMapSelector::m_TopTSE, CSeqMap_CI_SegmentInfo::m_TSE, SSeqMapSelector::SetFlags(), SSeqMapSelector::SetResolveCount(), ct::sort(), CSeqMap::x_GetChunkToLoad(), CSeqMap_CI::x_GetSegment(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap_CI::x_GetSeqMap(), and SSeqMapSelector::x_HasLimitTSE().
Referenced by CSeqVector_CI::CanGetRange(), CSeqMap::CanResolveRange(), CAsn2FastaApp::HandleSeqEntry(), LoadSequencesToScope(), CNewCleanup_imp::ProtSeqBC(), and CFastaOstream::WriteSequence().
◆ CanResolveRange() [2/2] ◆ ChangeSwitchPoint() void CSeqMapSwitchPoint::ChangeSwitchPoint ( TSeqPos pos, TSeqPos add )Definition at line 498 of file seq_map_switch.cpp.
References _ASSERT, CSeqMap::eSeqRef, CSeqMap::FindSegment(), CRange_Base::GetFrom(), CSeqMapSwitchPoint::GetInsert(), CSeqMap_CI::GetLength(), CSeqMapSwitchPoint::GetLengthDifference(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CSeqMap_CI::GetRefSeqid(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CRange_Base::GetTo(), CSeqMap_CI::GetType(), len, CSeqMapSwitchPoint::m_LeftId, CSeqMapSwitchPoint::m_LeftMinusStrand, CSeqMapSwitchPoint::m_LeftPos, CSeqMapSwitchPoint::m_Master, CSeqMapSwitchPoint::m_MasterPos, CSeqMapSwitchPoint::m_MasterRange, CSeqMapSwitchPoint::m_RightId, CSeqMapSwitchPoint::m_RightMinusStrand, CSeqMapSwitchPoint::m_RightPos, NCBI_THROW, and CSeqMap::SetSegmentRef().
◆ CloneFor() ◆ CNcbi2naRandomizer() CNcbi2naRandomizer::CNcbi2naRandomizer ( CRandom & gen ) ◆ CountSegmentsOfType() size_t CSeqMap::CountSegmentsOfType ( ESegmentType type ) const ◆ CreateSeqMapForBioseq() ◆ CreateSeqMapForSeq_loc()Definition at line 1134 of file seq_map.cpp.
References CSeqMap::CSeqMap(), CSeq_inst_Base::eMol_not_set, CSeqMap::eSeqEnd, CSeqMap::eSeqRef, CScope::GetBioseqHandle(), CBioseq_Handle::GetSequenceType(), i, CSeqMap::m_Mol, CSeqMap::CSegment::m_SegType, CSeqMap::x_GetRefSeqid(), and CSeqMap::x_GetSegment().
Referenced by GetSequenceFromLoc(), CAsn2FastaApp::HandleSeqEntry(), s_CreateGapMapIter(), s_SeqMapForHandle(), and CFlatGatherer::x_GatherReferences().
◆ CSegment() [1/2] ◆ CSegment() [2/2] ◆ CSeqMap() [1/6]Definition at line 202 of file seq_map.cpp.
References CSeq_ext_Base::e_Delta, CSeq_ext_Base::e_Map, CSeq_ext_Base::e_Ref, CSeq_ext_Base::e_Seg, CSeq_inst_Base::eRepr_map, CSeq_inst_Base::eRepr_not_set, CSeq_inst_Base::eRepr_virtual, CDelta_ext_Base::Get(), CSeg_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetMol(), CSeq_ext_Base::GetRef(), CSeq_inst_Base::GetRepr(), CSeq_ext_Base::GetSeg(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsGap(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetLength(), CSeq_inst_Base::IsSetMol(), CSeq_inst_Base::IsSetSeq_data(), ITERATE, kInvalidSeqPos, CSeqMap::m_Mol, CSeqMap::m_SeqLength, NCBI_THROW, CSeq_ext_Base::Which(), CSeqMap::x_Add(), CSeqMap::x_AddEnd(), and CSeqMap::x_AddGap().
◆ CSeqMap() [2/6] ◆ CSeqMap() [3/6] ◆ CSeqMap() [4/6] CSeqMap::CSeqMap ( CSeqMap * parent, size_t index ) protectedDefinition at line 130 of file seq_map.cpp.
◆ CSeqMap() [5/6] ◆ CSeqMap() [6/6] CSeqMap::CSeqMap ( void ) protected ◆ CSeqVector() [1/8] ◆ CSeqVector() [2/8] ◆ CSeqVector() [3/8] ◆ CSeqVector() [4/8] ◆ CSeqVector() [5/8] ◆ CSeqVector() [6/8] ◆ CSeqVector() [7/8] ◆ CSeqVector() [8/8] ◆ empty() bool CSeqVector::empty ( void ) const inline ◆ end() [1/2] ◆ End() ◆ end() [2/2]Definition at line 305 of file seq_vector.hpp.
References CSeqVector::CSeqVector_CI, and CSeqVector::size().
Referenced by CSplignFormatter::AsAlignmentText(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CChain::CollectTrustedmRNAsProts(), CAnnotCompare::CompareFeats(), variation::FindSSRLoc(), CInternalStopFinder::FindStartStopRanges(), CInternalStopFinder::GetCDSNucleotideSequence(), CBlastSeqVectorOM::GetCompressedPlusStrand(), CPostProcessUtils::GetLiteralAtLoc(), GetProteinWeight(), s_GetPolyA_genomic_priming(), variation_ref::CHgvsParser::CContext::Validate(), CAgpFastaComparator::CTmpSeqVecStorage::WriteData(), CFeatureItem::x_AddQualsProt(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CVariationUtilities::x_GetAlleleFromLoc(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), variation::CVariationUtil::x_InferNAfromAA(), variation_ref::CHgvsParser::x_LocToSeqStr(), variation::CHgvsParser::x_LocToSeqStr(), variation_ref::CVariationUtil::x_ProtToPrecursor(), and CValidError_graph::x_ValidateGraphValues().
◆ EndResolved() [1/2] ◆ EndResolved() [2/2] ◆ FindResolved() ◆ FindSegment() ◆ GetAllSwitchPoints() [1/2] ◆ GetAllSwitchPoints() [2/2] ◆ GetCoding() ◆ GetDifferences() ◆ GetGapChar() ◆ GetGapSeq_literal() ◆ GetGapSizeForward() ◆ GetInsert()Definition at line 450 of file seq_map_switch.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), CRange_Base::GetFrom(), CRange_Base::GetTo(), CSeqMapSwitchPoint::m_LeftDifferences, CSeqMapSwitchPoint::m_Master, CSeqMapSwitchPoint::m_MasterPos, CSeqMapSwitchPoint::m_MasterRange, CSeqMapSwitchPoint::m_RightDifferences, NCBI_THROW, and offset.
Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().
◆ GetLeftInPlaceInsert() TSeqPos CSeqMapSwitchPoint::GetLeftInPlaceInsert ( void ) const ◆ GetLength()Definition at line 482 of file seq_map.hpp.
References kInvalidSeqPos, CSeqMap::m_SeqLength, CSeqMap::x_GetLastEndSegmentIndex(), and CSeqMap::x_GetSegmentPosition().
Referenced by AgpWrite(), CSeqMap::CanResolveRange(), CSeqVector::CSeqVector(), CBioseq_Handle::GetBioseqLength(), CBioseq_Info::GetInst_Length(), CSeqMap::HasZeroGapAt(), CSeqMap::x_DoUpdateSeq_inst(), CSeqVector_CI::x_GetSize(), CSeqMap::x_ResolveSegmentLength(), and CSeqMap_CI::x_Select().
◆ GetLengthDifference() int CSeqMapSwitchPoint::GetLengthDifference ( TSeqPos new_pos, TSeqPos add =0 ) const inline ◆ GetMol() ◆ GetMutex() ◆ GetPackedSeqData()
Definition at line 311 of file seq_vector.cpp.
References CSeqVector::CanGetRange(), CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqVector::GetCoding(), CSeqVector::m_TSE, min(), NCBI_THROW_FMT, CSeqVector::size(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), and CSeqVector::x_GetPacked8SeqData().
Referenced by CBlastSequenceSource::GetSeq(), and CSequenceAmbigTrimmer::x_SliceBioseq().
◆ GetRightInPlaceInsert() TSeqPos CSeqMapSwitchPoint::GetRightInPlaceInsert ( void ) const ◆ GetScope() CScope & CSeqVector::GetScope ( void ) const inline ◆ GetSegmentsCount() size_t CSeqMap::GetSegmentsCount ( void ) const inline ◆ GetSeqData() [1/2] ◆ GetSeqData() [2/2]Fill the buffer string with the sequence data for the interval [start, stop).
Definition at line 304 of file seq_vector.cpp.
References buffer, CSeqVector::GetMutex(), CSeqVector_CI::GetSeqData(), and CSeqVector::x_GetIterator().
Referenced by CSAM_CIGAR_Formatter::AddRow(), CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CExpandGaps::apply(), CSplignFormatter::AsAlignmentText(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CEquivRangeBuilder::CalcMatches(), CAlnVec::CalculateScore(), CPrefetchSeqData::Execute(), ExtendLocationForTranslExcept(), CFindRSites::Find(), variation::FindSSRLoc(), CInternalStopFinder::FindStartStopRanges(), COrf::FindStrongKozakUOrfs(), CFlatAnticodonQVal::Format(), g_ConvertDeltaToRawSeq(), CScore_SegPct::Get(), CScore_Entropy::Get(), NSnp::GetAlleles(), CAlnVec::GetAlnSeqString(), CSparseAlignment::GetAlnSeqString(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CProjectedMappingInfo::GetAnchorSequence(), CInternalStopFinder::GetCDSNucleotideSequence(), CAlnVec::GetColumnVector(), CAddGlobalCodeBreak::GetCommand(), CEditSequenceEnds::GetCommand(), CBlastSeqVectorOM::GetCompressedPlusStrand(), GetDNASequence(), CEditSequence::GetFeatures(), CFlatFileGenerator::GetFTableAnticodonText(), CSimpleOM::GetIupac(), CPostProcessUtils::GetLiteralAtLoc(), GetLoc(), GetProteinString(), CAlnVec::GetResidue(), CPaintAlignment::GetSegments(), CSeqVectorCache::GetSeq(), CSeqVector::GetSeqData(), GetSeqsStatus(), CAlnWriter::GetSeqString(), CGuiObjectInfoSeq_align::GetSeqString(), CDensegGraphicDataSource::GetSeqString(), CAlnVec::GetSeqString(), CAlnMixSeq::GetSeqString(), CSparseAln::GetSeqString(), CSparseAlignment::GetSeqString(), CBioseqIndex::GetSequence(), CFeatureIndex::GetSequence(), CEditingActionFeatTranslation::GetValue(), sequpd::HaveIdenticalResidues(), CAlignCollapser::CPartialString::Init(), IsExtendableLeft(), IsExtendableRight(), CGuiObjectInfoSeq_align::IsPolyA(), CSeqTextDataSourceInterval::LookForSpliceJunctions(), CRestoreRNAediting::OnApply(), CFlatFileSeqBlockIterator::operator*(), CTabularFormatter_MismatchPositions::Print(), RemoteFetchLongNucleotideBioseq(), CHitMatrixSeqGraph::Render(), RetrievePartsOfLargeChromosome(), CAlnVec::RetrieveSegmentSequences(), CDemoApp::Run(), CSampleObjmgrApplication::Run(), CTestSingleAln_All::RunTest(), CTestTranscript_PolyA::RunTest(), s_CdsStartCodon(), s_CdsStopCodon(), s_CodonVariation(), CUpdateSeq_Input::s_ConvertDeltaToRawBioseq(), s_CountAmbiguities(), s_DumpSequences_wRange(), CSequenceUpdater::s_ExtendOneEndOfSequence(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetPolyA_genomic_priming(), s_GetQuerySequence(), s_GetSplicedSegIdentityMismatch(), s_OrfExtension(), s_RunBlast2NWSeq(), ScanForCpGs(), SeqLocToBioseq(), CSeqUtils::SeqLocToBioseq(), CIgBlastTabularInfo::SetAirrFormatData(), CMultAlign::SetGenomic(), CIgBlastTabularInfo::SetIgAnnotation(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CCDSTranslationPanel::TransferDataToWindow(), TrimStopsFromCompleteCDS(), UpdateSeqLength(), CAssemblyGapValidator::Validate(), CGapFeatValidator::Validate(), variation_ref::CHgvsParser::CContext::Validate(), CProductStringBuilder::x_AddExon(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualTranslation(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CSingleFeatValidator::x_CalculateLocationGaps(), CSGAlignStatJob::x_CollectAlignStats(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CWriteDB_Impl::x_CookSequence(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSGAlignStatJob::x_CreatePileUpGraphs(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CURLTooltipHandler::x_DisplayForwardStrandRegion(), CURLTooltipHandler::x_DisplayReverseStrandRegion(), CCpgSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CCdsGlyph::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFeatGlyph::x_DrawRNAProductSequence(), CAlignGlyph::x_DrawUnalignedRowSequence(), CSFTranslationJob::x_Execute(), CSequenceUpdater::x_ExtendOneEnd(), CVariationUtilities::x_GetAlleleFromLoc(), CDensegGraphicDataSource::x_GetAlnStringFromCigar(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CCrossPanelIR::x_GetSequence(), x_GetSequence(), CSequenceSearchJob::x_GetSequence(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CPrimaryItem::x_GetStrForPrimary(), CPsiBlastInputData::x_GetSubjectSequence(), CCDSTranslationProblems::x_GetTranslExceptProblems(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), variation::CVariationUtil::x_InferNAfromAA(), CSingleFeatValidator::x_IsMostlyNs(), CSplign::x_LoadSequence(), variation_ref::CHgvsParser::x_LocToSeqStr(), variation::CHgvsParser::x_LocToSeqStr(), CSequenceUpdater::x_PatchSequence(), CAgpFastaComparator::x_Process(), CSplignApp::x_ProcessPair(), CPromote::x_PromoteRna(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CUpdateSeq_Input::x_ReadAccession(), CSequenceTrack::x_RenderSequence(), CFastaSeqBlockItem::x_RenderText(), CSequenceUpdater::x_ReplaceSequence(), CInstancedAligner::x_RunMMGlobal(), CSequenceSearchJob::x_SearchSequence(), CVectorTrimPanel::x_SetSeqData(), CUnorderedSplitter::x_SplitSeqData(), CCdregionValidator::x_ValidateConflict(), CCdregionValidator::x_ValidateFeatComment(), CSingleFeatValidator::x_ValidateReplaceQual(), CSingleFeatValidator::x_ValidateRptUnitVal(), and CVcfWriter::x_WriteFeature().
◆ GetSeqMap() ◆ GetSeqMapForSeq_loc()Definition at line 1162 of file seq_map.cpp.
References ConstRef(), CSeqMap::CSeqMap(), CSeq_inst_Base::eMol_not_set, CSeqMap::eSeqEnd, CSeqMap::eSeqRef, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetSequenceType(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::GetWhole(), i, CSeq_loc_Base::IsInt(), IsReverse(), CSeq_interval_Base::IsSetStrand(), CSeq_loc_Base::IsWhole(), CSeqMap::m_Mol, CSeqMap::CSegment::m_SegType, CSeqMap::x_GetRefSeqid(), and CSeqMap::x_GetSegment().
Referenced by CFeatGapInfo::CollectGaps(), CSplign::x_LoadSequence(), and CSplign::x_RunOnCompartment().
◆ GetSequenceDifference() int CSeqMapSwitchPoint::GetSequenceDifference ( TSeqPos new_pos, TSeqPos add =0 ) const inline ◆ GetSequenceType() ◆ GetStrand() ◆ GetSwitchPoint() ◆ HasSegmentOfType() ◆ HasZeroGapAt()
Returns true if there is zero-length gap at position.
Checks referenced sequences too.
Definition at line 907 of file seq_map.cpp.
References _ASSERT, CSeqMap::eSeqGap, CSeqMap::eSeqRef, CSeqMap::GetLength(), CSeqMap::HasZeroGapAt(), CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefMinusStrand, CSeqMap::CSegment::m_RefPosition, CSeqMap::CSegment::m_SegType, CSeqMap::x_FindSegment(), CSeqMap::x_GetFirstEndSegmentIndex(), CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegment(), and CSeqMap::x_GetSubSeqMap().
Referenced by CSeqMap::HasZeroGapAt(), and CSeqVector_CI::HasZeroGapBefore().
◆ InsertInPlace() void CSeqMapSwitchPoint::InsertInPlace ( TSeqPos add_left, TSeqPos add_right ) ◆ InsertSegmentGap()Insert new gap into sequence map.
Definition at line 723 of file seq_map.cpp.
References _ASSERT, CSeqMap::CSeqMap_CI, CSeqMap::eSeqGap, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_Segments, CSeqMap::m_SeqMap_Mtx, CSeqMap_CI_SegmentInfo::x_GetIndex(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap::x_GetSegmentPosition(), CSeqMap_CI_SegmentInfo::x_GetSeqMap(), CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().
Referenced by CSeqMap_I::InsertGap().
◆ IsInGap()true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe, do not call it in parallel with other, even MT-safe method.
It will be MT-safe to call this method after locking GetMutex().
Definition at line 277 of file seq_vector.hpp.
References CSeqVector_CI::IsInGap(), and CSeqVector::x_GetIterator().
Referenced by CConvertGapsBySize::apply(), CExpandGaps::apply(), CCombineAdjacentGaps::apply_impl(), CheckBioseqEndsForNAndGap(), CAddLinkageToGaps::GetCommand(), HasBadProteinStart(), CAlignCollapser::InitContig(), CSpliceProblems::ReadAcceptorSpliceSite(), CSpliceProblems::ReadDonorSpliceSite(), CDemoApp::Run(), s_AfterIsGap(), s_BeforeIsGap(), s_CheckPosNOrGap(), s_PartialAtGapOrNs(), s_PosIsNNotGap(), StartAbutsGap(), StopAbutsGap(), CSeqTranslator::TranslateToProtein(), CIntronValidator::Validate(), CGapFeatValidator::Validate(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::x_CalculateNsStretchAndTotal(), CCdregionValidator::x_CheckPosNOrGap(), CCDSTranslationProblems::x_Is5AtEndSpliceSiteOrGap(), CReportTrim::x_IsThereGapNotAtTheEnd(), and CFeatureGenerator::SImplementation::x_MapFeature().
◆ IsNucleotide() bool CSeqVector::IsNucleotide ( void ) const inline ◆ IsProtein() bool CSeqVector::IsProtein ( void ) const inlineDefinition at line 350 of file seq_vector.hpp.
References CSeqVector::GetSequenceType(), and CSeq_inst::IsAa().
Referenced by CPostProcessUtils::GetLiteralAtLoc(), s_ReadAndTestQueryFromString(), SeqLocToBioseq(), CSeqUtils::SeqLocToBioseq(), CSeqVector::SetIupacCoding(), CSeqVector::SetNcbiCoding(), CFastaOstream::Write(), CFastaOstream::WriteSequence(), CSequenceDataTester::x_CompareSequenceData(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CAlnVec::x_GetSeqVector(), CSparseAln::x_GetSeqVector(), CSequenceDataTester::x_TestSingleNucleotide_Remote(), CSequenceDataTester::x_TestSingleProtein_Remote(), and CFastaOstream::x_WriteSequence().
◆ IsSetData() bool CSeqMap::CSegment::IsSetData ( void ) const inline ◆ LoadSeq_data() ◆ operator()() [1/3] ◆ operator()() [2/3] ◆ operator()() [3/3] ◆ operator<() ◆ operator=() [1/3] ◆ operator=() [2/3] ◆ operator=() [3/3]Definition at line 244 of file seq_vector.cpp.
References CSeqVector::GetMutex(), CSeqVector::m_Coding, CSeqVector::m_Iterator, CSeqVector::m_Mol, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Size, CSeqVector::m_Strand, CSeqVector::m_TSE, and AutoPtr< X, Del >::reset().
◆ operator[]()0-based array of residues Note: this method is not MT-safe, do not call it in parallel with other, even MT-safe method.
It will be MT-safe to call this method after locking GetMutex().
Definition at line 270 of file seq_vector.hpp.
References CSeqVector::x_GetIterator().
◆ RandomizeData() void CNcbi2naRandomizer::RandomizeData ( char * buffer, size_t count, TSeqPos pos ) virtual ◆ RemoveSegment()Delete segment from sequence map.
Definition at line 740 of file seq_map.cpp.
References _ASSERT, CSeqMap::CSeqMap_CI, CSeqMap::eSeqEnd, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_Segments, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap_CI_SegmentInfo::x_GetIndex(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap::x_GetSegmentPosition(), CSeqMap_CI_SegmentInfo::x_GetSeqMap(), CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().
Referenced by CSeqMap_I::Remove().
◆ ResetMol() void CSeqMap::ResetMol ( void ) ◆ ResetRepr() void CSeqMap::ResetRepr ( void ) ◆ ResolveAll() void CSeqMap::ResolveAll ( void ) const private ◆ ResolvedRangeIterator()Iterate segments in the range with specified strand coordinates.
Definition at line 868 of file seq_map.cpp.
References CSeqMap::CSeqMap_CI, flags, SSeqMapSelector::SetFlags(), SSeqMapSelector::SetRange(), SSeqMapSelector::SetResolveCount(), and SSeqMapSelector::SetStrand().
Referenced by CFeatGapInfo::CollectGaps(), CTextItemSeq_loc::CreateObject(), CGapInfo< CBlastTabular >::IntersectsNonBridgeableGap(), CDemoApp::Run(), TrimSeqData(), CComponentSearchJob::x_DoSearch(), CSplign::x_RunOnCompartment(), CVectorTrimPanel::x_SetSeqData(), and CSequenceAmbigTrimmer::x_SliceBioseq().
◆ SetCoding() [1/2] ◆ SetCoding() [2/2] void CSeqVector::SetCoding ( TCoding coding )Definition at line 1272 of file seq_vector.cpp.
References CSeqVector::m_Coding, and CSeqVector::x_ResetIterator().
Referenced by CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CCDSTranslationProblems::CalculateTranslationProblems(), CSeqVector::CSeqVector(), CPrefetchSeqData::Execute(), CScore_SegPct::Get(), GetMismatches(), GetProteinString(), GetProteinWeight(), GetProteinWeights(), CBlastSequenceSource::GetSeq(), CBioseqIndex::GetSequence(), CFeatureIndex::GetSequence(), CEditingActionFeatTranslation::GetValue(), MakeSeqVectorForResidueCounting(), CRestoreRNAediting::OnApply(), CUpdateSeq_Input::s_ConvertDeltaToRawBioseq(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetQuerySequence(), CBlastSeqVectorOM::SetCoding(), CSeqVector::SetCoding(), CSeqVector::SetIupacCoding(), CSeqVector::SetNcbiCoding(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CCDSTranslationPanel::TransferDataToWindow(), TrimStopsFromCompleteCDS(), CFastaOstream::Write(), CFastaOstream::WriteSequence(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualTranslation(), CFeaturePropagator::x_CdsStopAtStopCodon(), CSequenceDataTester::x_CompareSequenceData(), COrfSearchJob::x_DoSearch(), CSequenceItem::x_GatherInfo(), CAlnVec::x_GetSeqVector(), CSparseAln::x_GetSeqVector(), CPsiBlastInputData::x_GetSubjectSequence(), CSequenceUpdater::x_ReplaceSequence(), CSequenceDataTester::x_TestSingleNucleotide_Remote(), CSequenceDataTester::x_TestSingleProtein_Remote(), CCdregionValidator::x_ValidateConflict(), and CValidError_graph::x_ValidateGraphValues().
◆ SetIupacCoding() void CSeqVector::SetIupacCoding ( void )Set coding to either Iupacaa or Iupacna depending on molecule type.
Definition at line 1281 of file seq_vector.cpp.
References CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeqVector::IsProtein(), and CSeqVector::SetCoding().
Referenced by CContigAssembly::BandedGlobalAlignment(), CSimpleOM::GetIupac(), CCodingPropensity::GetScore(), CHitMatrixSeqGraph::Render(), CLocalFinderApp::Run(), CTestSingleAln_All::RunTest(), CTestTranscript_PolyA::RunTest(), CTestTranscript_Orfs::RunTest(), s_CdsStartCodon(), s_CdsStopCodon(), s_CompareProtProdToTrans(), s_CountAmbiguities(), s_InframeUpstreamStart(), s_InframeUpstreamStop(), s_OrfExtension(), s_PrematureStopCodon(), s_ReadAndTestQueryFromString(), CSeqVector::SetCoding(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CAlnVec::x_GetSeqVector(), CSparseAln::x_GetSeqVector(), and CFastaSeqBlockItem::x_RenderText().
◆ SetMol() ◆ SetNcbiCoding() void CSeqVector::SetNcbiCoding ( void ) ◆ SetNoAmbiguities() void CSeqVector::SetNoAmbiguities ( void ) ◆ SetRandomizeAmbiguities() [1/4] void CSeqVector::SetRandomizeAmbiguities ( CRandom & random_gen ) ◆ SetRandomizeAmbiguities() [2/4] ◆ SetRandomizeAmbiguities() [3/4] void CSeqVector::SetRandomizeAmbiguities ( Uint4 seed ) ◆ SetRandomizeAmbiguities() [4/4] void CSeqVector::SetRandomizeAmbiguities ( void ) ◆ SetRegionInChunk()Definition at line 1438 of file seq_map.cpp.
References _ASSERT, CSeqMap::eSeqData, CSeqMap::eSeqGap, kInvalidSeqPos, literal(), CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefObject, CSeqMap::m_Resolved, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqLength, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap::x_FindSegment(), CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegmentException(), CSeqMap::x_GetSeq_literal(), CSeqMap::x_SetChunk(), and CSeqMap::x_SetSegment().
Referenced by CTSE_Default_Assigner::AddSeq_data().
◆ SetRepr() ◆ SetSegmentData() ◆ SetSegmentGap() [1/2] ◆ SetSegmentGap() [2/2] ◆ SetSegmentRef() ◆ SetStrand() ◆ size() TSeqPos CSeqVector::size ( void ) const inlineDefinition at line 291 of file seq_vector.hpp.
References CSeqVector::m_Size.
Referenced by CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CEquivRangeBuilder::CalcMatches(), CalculateEffectiveTranslationLengths(), CAlnVec::CalculateScore(), CCDSTranslationProblems::CalculateTranslationProblems(), CdsTrnaOverlapStr(), CheckBioseqEndsForNAndGap(), Does3primerAbutGap(), CSeqVector::end(), ExtendCDSToStopCodon(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), CFindRSites::Find(), CInternalStopFinder::FindStartStopRanges(), COrf::FindStrongKozakUOrfs(), CFlatAnticodonQVal::Format(), CAlnVec::GetAlnSeqString(), CSparseAlignment::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CAlnVec::GetColumnVector(), CAddGlobalCodeBreak::GetCommand(), CExtendCDSToStop::GetCommand(), GetDNASequence(), CSimpleOM::GetIupac(), GetLoc(), GetMRNATranslationProblems(), CSRSearch::getNMer(), CSeqVector::GetPackedSeqData(), CNucProp::GetPercentGC(), CProtProp::GetProteinPI(), GetProteinWeights(), CAlnVec::GetResidue(), CCodingPropensity::GetScore(), CBlastSequenceSource::GetSeq(), CBlastSequenceSource::GetSeqLength(), CSeqVectorCache::GetSeqSize(), GetSeqsStatus(), CAlnVec::GetSeqString(), CAlnMixSeq::GetSeqString(), CSparseAln::GetSeqString(), CSparseAlignment::GetSeqString(), CBioseqIndex::GetSequence(), CFeatureIndex::GetSequence(), CEditingActionFeatTranslation::GetValue(), HasBadProteinStart(), CBlastBioseqMaker::HasSequence(), CAlignCollapser::InitContig(), CRestoreRNAediting::OnApply(), CTabularFormatter_MismatchPositions::Print(), RetrievePartsOfLargeChromosome(), CAlnVec::RetrieveSegmentSequences(), CDemoApp::Run(), CSampleObjmgrApplication::Run(), CTestSingleAln_All::RunTest(), CTestTranscript_PolyA::RunTest(), s_CdsStopCodon(), s_CodonVariation(), s_CompareProtProdToTrans(), s_CountAmbiguities(), s_DumpSequences_wRange(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetKozakStrength(), s_GetQuerySequence(), s_PartialAtGapOrNs(), s_PosIsNNotGap(), s_PrematureStopCodon(), s_ReadAndTestQueryFromString(), s_RunBlast2NWSeq(), ScanForCpGs(), CSeqSearch::Search(), CSRSearch_Impl< index_t >::search(), CSRSearch_Impl< index_t >::searchOneMismatch(), SeqLocToBioseq(), CSeqUtils::SeqLocToBioseq(), CMultAlign::SetGenomic(), SSeqDB_SVCISource::SSeqDB_SVCISource(), StopAbutsGap(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CCDSTranslationPanel::TransferDataToWindow(), CSeqTranslator::TranslateToProtein(), TrimStopsFromCompleteCDS(), CGapFeatValidator::Validate(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualTranslation(), CSingleFeatValidator::x_CalculateLocationGaps(), CValidError_bioseq::x_CalculateNsStretchAndTotal(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CSequenceDataTester::x_CompareSequenceData(), CWriteDB_Impl::x_ComputeSeqLength(), CWriteDB_Impl::x_CookSequence(), CCDSTranslationProblems::x_CountTerminalXs(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CURLTooltipHandler::x_DisplayForwardStrandRegion(), CURLTooltipHandler::x_DisplayReverseStrandRegion(), CCpgSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CCdsGlyph::x_Draw(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFeatGlyph::x_DrawRNAProductSequence(), CFeaturePropagator::x_ExtendToStopCodon(), CBioseqGaps_CI::x_FindNextGapOnBioseq(), CBaseCountItem::x_GatherInfo(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), x_GetSequence(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CSingleFeatValidator::x_IsMostlyNs(), CSplign::x_LoadSequence(), CFeatureGenerator::SImplementation::x_MapFeature(), CSplignApp::x_ProcessPair(), CPromote::x_PromoteRna(), CInstancedAligner::x_RunMMGlobal(), CSequenceSearchJob::x_SearchSequence(), CFeatureGenerator::SImplementation::x_SetComment(), CReportEntry::x_SetSequence(), CSeqVector_CI::x_SetVector(), CBlastSeqVectorOM::x_Size(), CUnorderedSplitter::x_SplitSeqData(), CSequenceDataTester::x_TestSingleNucleotide_Remote(), CSequenceDataTester::x_TestSingleProtein_Remote(), CCdregionValidator::x_ValidateConflict(), CSingleFeatValidator::x_ValidateReplaceQual(), and CSingleFeatValidator::x_ValidateRptUnitVal().
◆ x_Add() [1/12] ◆ x_Add() [2/12] ◆ x_Add() [3/12] ◆ x_Add() [4/12] ◆ x_Add() [5/12] ◆ x_Add() [6/12] ◆ x_Add() [7/12]Definition at line 1359 of file seq_map.cpp.
References CSeq_literal_Base::CanGetFuzz(), CInt_fuzz_Base::eLim_unk, CSeq_literal_Base::GetFuzz(), CSeq_literal_Base::GetLength(), CInt_fuzz_Base::GetLim(), CSeq_literal_Base::GetSeq_data(), CSeq_data_Base::IsGap(), CInt_fuzz_Base::IsLim(), CSeq_literal_Base::IsSetSeq_data(), CSeqMap::x_Add(), and CSeqMap::x_AddGap().
◆ x_Add() [8/12]Definition at line 1380 of file seq_map.cpp.
References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_Base::GetEquiv(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_loc_Base::GetWhole(), NCBI_THROW, CSeq_loc_Base::Which(), CSeqMap::x_Add(), and CSeqMap::x_AddGap().
◆ x_Add() [9/12] ◆ x_Add() [10/12] ◆ x_Add() [11/12] ◆ x_Add() [12/12] ◆ x_AddEnd() void CSeqMap::x_AddEnd ( void ) protected ◆ x_AddGap() [1/3] void CSeqMap::x_AddGap ( TSeqPos len, bool unknown_len ) protected ◆ x_AddGap() [2/3] ◆ x_AddGap() [3/3] ◆ x_AddSegment() [1/3] ◆ x_AddSegment() [2/3] ◆ x_AddSegment() [3/3] ◆ x_AddUnloadedSeq_data() void CSeqMap::x_AddUnloadedSeq_data ( TSeqPos len ) protected ◆ x_CreateIterator() ◆ x_DoUpdateSeq_inst()Definition at line 1494 of file seq_map.cpp.
References _ASSERT, data, delta(), CInt_fuzz_Base::eLim_unk, eNa_strand_minus, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_virtual, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::eSeqLiteral, CSeqMap::eSeqRef, CSeq_inst_Base::GetExt(), CSeqMap::GetLength(), CSeqMap::GetSegmentsCount(), CSeqMap::HasSegmentOfType(), CSeq_ext_Base::IsSeg(), CSeq_inst_Base::IsSetExt(), CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefMinusStrand, CSeqMap::CSegment::m_RefPosition, CSeqMap::CSegment::m_SegType, CSeqMap::CSegment::m_UnknownLength, CSeq_inst_Base::ResetExt(), CSeq_literal_Base::ResetFuzz(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_inst_Base::ResetSeq_data(), CSeq_literal_Base::ResetSeq_data(), CSeq_interval_Base::ResetStrand(), CSeq_inst_Base::SetExt(), CSeq_interval_Base::SetFrom(), CSeq_literal_Base::SetFuzz(), CSeq_interval_Base::SetId(), CSeq_loc::SetInt(), CSeq_inst_Base::SetLength(), CSeq_literal_Base::SetLength(), CDelta_seq_Base::SetLiteral(), CDelta_seq_Base::SetLoc(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), CSeq_literal_Base::SetSeq_data(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), CSeqMap::x_GetFirstEndSegmentIndex(), CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetRefSeqid(), CSeqMap::x_GetSegmentLength(), CSeqMap::x_GetSeq_data(), CSeqMap::x_GetSeq_literal(), and CSeqMap::x_SetSegment().
Referenced by CSeqMap::x_UpdateSeq_inst().
◆ x_FindSegment() size_t CSeqMap::x_FindSegment ( TSeqPos position, CScope * scope ) const protectedDefinition at line 403 of file seq_map.cpp.
References kInvalidSeqPos, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_Segments, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegment(), and CSeqMap::x_GetSegmentLength().
Referenced by CSeqMap::HasZeroGapAt(), CSeqMap::LoadSeq_data(), CSeqMap::SetRegionInChunk(), and CSeqMap_CI::x_Push().
◆ x_GetBioseqInfo() ◆ x_GetChunkToLoad()Definition at line 461 of file seq_map.cpp.
References _ASSERT, CSeqMap::eSeqChunk, CConstRef< C, Locker >::GetPointer(), kInvalidSeqPos, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, and CTSE_Chunk_Info::NotLoaded().
Referenced by CSeqMap::CanResolveRange().
◆ x_GetFirstEndSegmentIndex() size_t CSeqMap::x_GetFirstEndSegmentIndex ( void ) const inlineprotected ◆ x_GetIterator() ◆ x_GetLastEndSegmentIndex() size_t CSeqMap::x_GetLastEndSegmentIndex ( void ) const inlineprotected ◆ x_GetObject() ◆ x_GetPacked2naSeqData()Definition at line 983 of file seq_vector.cpp.
References _ASSERT, count, data, CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeqVectorTypes::eCaseConversion_none, CSeqMap::eSeqGap, CSeqMap::fDefaultFlags, CSeqVector::GetCoding(), CSeqMap_CI::GetEndPosition(), CRef< C, Locker >::GetPointer(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefData(), CSeqMap_CI::GetRefEndPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CHeapScope::GetScopeOrNull(), CSeqMap_CI::GetType(), kMax_UInt, CSeqVector::m_Randomizer, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Strand, CSeqVector::m_TSE, min(), NCBI_THROW, NCBI_THROW_FMT, SSeqMapSelector::SetLinkUsedTSE(), SSeqMapSelector::SetStrand(), CSeqVectorTypes::sm_TrivialTable, CSeqVectorTypes::sx_GetConvertTable(), CSeqVectorTypes::sx_GetGapChar(), table, x_Append2To2(), x_AppendAnyTo2(), and x_AppendRandomTo2().
Referenced by CSeqVector::GetPackedSeqData().
◆ x_GetPacked4naSeqData()Definition at line 912 of file seq_vector.cpp.
References _ASSERT, count, data, CSeqVectorTypes::eCaseConversion_none, CSeqMap::eSeqGap, CSeqMap::fDefaultFlags, CSeqVector::GetCoding(), CSeqMap_CI::GetEndPosition(), CSeqVector::GetGapChar(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefData(), CSeqMap_CI::GetRefEndPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CHeapScope::GetScopeOrNull(), CSeqMap_CI::GetType(), kMax_UInt, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Strand, CSeqVector::m_TSE, min(), NCBI_THROW_FMT, SSeqMapSelector::SetLinkUsedTSE(), SSeqMapSelector::SetStrand(), CSeqVectorTypes::sm_TrivialTable, CSeqVectorTypes::sx_GetConvertTable(), table, x_Append4To4(), x_AppendAnyTo4(), and x_AppendGapTo4().
Referenced by CSeqVector::GetPackedSeqData().
◆ x_GetPacked8SeqData()Definition at line 821 of file seq_vector.cpp.
References _ASSERT, _DEBUG_ARG, count, data, CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqVectorTypes::eCaseConversion_none, CSeqMap::eSeqGap, CSeqMap::fDefaultFlags, CSeqVector::GetCoding(), CSeqMap_CI::GetEndPosition(), CSeqVector::GetGapChar(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefData(), CSeqMap_CI::GetRefEndPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CHeapScope::GetScopeOrNull(), CSeqMap_CI::GetType(), kMax_UInt, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Strand, CSeqVector::m_TSE, min(), NCBI_THROW_FMT, SSeqMapSelector::SetLinkUsedTSE(), SSeqMapSelector::SetStrand(), CSeqVectorTypes::sm_TrivialTable, CSeqVectorTypes::sx_GetConvertTable(), table, x_Append8To8(), x_AppendAnyTo8(), and x_AppendGapTo8().
Referenced by CSeqVector::GetPackedSeqData().
◆ x_GetRefMinusStrand() ◆ x_GetRefPosition() ◆ x_GetRefSeqid() ◆ x_GetSegment()Definition at line 447 of file seq_map.hpp.
References _ASSERT, and CSeqMap::m_Segments.
Referenced by CSeqMap::CreateSeqMapForSeq_loc(), CSeqMap::GetSeqMapForSeq_loc(), CSeqMap::HasZeroGapAt(), CSeqMap::LoadSeq_data(), CSeqMap::x_FindSegment(), CSeqMap_CI_SegmentInfo::x_GetSegment(), CSeqMap::x_GetSegmentLength(), CSeqMap_CI_SegmentInfo::x_Move(), CSeqMap::x_ResolveSegmentLength(), and CSeqMap::x_ResolveSegmentPosition().
◆ x_GetSegmentEndPosition() TSeqPos CSeqMap::x_GetSegmentEndPosition ( size_t index, CScope * scope ) const inlineprotected ◆ x_GetSegmentException() void CSeqMap::x_GetSegmentException ( size_t index ) const protected ◆ x_GetSegmentLength() TSeqPos CSeqMap::x_GetSegmentLength ( size_t index, CScope * scope ) const inlineprotected ◆ x_GetSegmentPosition() TSeqPos CSeqMap::x_GetSegmentPosition ( size_t index, CScope * scope ) const inlineprotected ◆ x_GetSeq_data() ◆ x_GetSeq_literal() ◆ x_GetSequenceClass() int CSeqMap::x_GetSequenceClass ( void ) const protected ◆ x_GetSubSeqMap() ◆ x_InitRandomizer() void CSeqVector::x_InitRandomizer ( CRandom & random_gen ) private ◆ x_InitSequenceType() void CSeqVector::x_InitSequenceType ( void ) private ◆ x_IsChanged() bool CSeqMap::x_IsChanged ( void ) const inlineprotected ◆ x_LoadObject()Definition at line 442 of file seq_map.cpp.
References _ASSERT, CSeqMap::eSeqChunk, CConstRef< C, Locker >::GetPointer(), kInvalidSeqPos, CTSE_Chunk_Info::Load(), CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, and CSeqMap::m_SeqMap_Mtx.
Referenced by CSeqMap::x_GetObject().
◆ x_ResetIterator() void CSeqVector::x_ResetIterator ( void ) const private ◆ x_ResolveSegmentLength() TSeqPos CSeqMap::x_ResolveSegmentLength ( size_t index, CScope * scope ) const protectedDefinition at line 343 of file seq_map.cpp.
References CSeqMap::eSeqRef, CSeqMap::eSeqSubMap, CTSE_Info::FindMatchingBioseq(), CBioseq_Info::GetBioseqLength(), CSeq_id_Handle::GetHandle(), CSeqMap::GetLength(), CTSE_Info_Object::GetTSE_Info(), kInvalidSeqPos, CSeqMap::m_Bioseq, CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_SegType, NCBI_THROW, CSeqMap::x_GetBioseqInfo(), CSeqMap::x_GetRefSeqid(), CSeqMap::x_GetSegment(), and CSeqMap::x_GetSubSeqMap().
Referenced by CSeqMap::x_GetSegmentLength().
◆ x_ResolveSegmentPosition() TSeqPos CSeqMap::x_ResolveSegmentPosition ( size_t index, CScope * scope ) const protected ◆ x_SetChanged() void CSeqMap::x_SetChanged ( size_t index ) protectedDefinition at line 597 of file seq_map.cpp.
References kInvalidSeqPos, CSeqMap::m_Bioseq, CSeqMap::m_Changed, CSeqMap::m_HasSegments, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_SeqLength, CBioseq_Info::x_SetChangedSeqMap(), and CSeqMap::x_SetSegment().
Referenced by CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().
◆ x_SetChunk() ◆ x_SetObject() ◆ x_SetSegment() ◆ x_SetSegmentData() void CSeqMap::x_SetSegmentData ( size_t index, TSeqPos length, CSeq_data & data ) protectedDefinition at line 647 of file seq_map.cpp.
References data, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().
Referenced by CSeqMap::SetSegmentData().
◆ x_SetSegmentGap() void CSeqMap::x_SetSegmentGap ( size_t index, TSeqPos length, CSeq_data * gap_data =0 ) protected
Definition at line 626 of file seq_map.cpp.
References CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeq_data_Base::IsGap(), CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().
Referenced by CSeqMap::SetSegmentGap().
◆ x_SetSegmentRef()Definition at line 662 of file seq_map.cpp.
References CSeqMap::eSeqRef, CConstRef< C, Locker >::GetPointer(), CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefMinusStrand, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_RefPosition, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().
Referenced by CSeqMap::SetSegmentRef().
◆ x_SetSeq_data() void CSeqMap::x_SetSeq_data ( size_t index, CSeq_data & data ) protected ◆ x_SetSubSeqMap() void CSeqMap::x_SetSubSeqMap ( size_t index, CSeqMap_Delta_seqs * subMap ) protected ◆ x_StartEditing() void CSeqMap::x_StartEditing ( void ) protected ◆ x_UpdateSeq_inst() ◆ ~CNcbi2naRandomizer() CNcbi2naRandomizer::~CNcbi2naRandomizer ( void )Definition at line 107 of file seq_vector.cpp.
◆ ~CSeqMap() CSeqMap::~CSeqMap ( void ) ◆ ~CSeqVector() CSeqVector::~CSeqVector ( void ) virtualDefinition at line 239 of file seq_vector.cpp.
◆ m_Bioseq ◆ m_Changed ◆ m_Coding ◆ m_Delta ◆ m_ExactMasterRange ◆ m_FirstAlign ◆ m_FixedTable char CNcbi2naRandomizer::m_FixedTable[16] private ◆ m_HasSegments ◆ m_Iterator ◆ m_IteratorMutex TMutex CSeqVector::m_IteratorMutex mutableprivate ◆ m_LeftDifferences ◆ m_LeftId ◆ m_LeftMinusStrand bool CSeqMapSwitchPoint::m_LeftMinusStrand ◆ m_LeftPos TSeqPos CSeqMapSwitchPoint::m_LeftPos ◆ m_Length atomic<TSeqPos> CSeqMap::CSegment::m_Length mutableDefinition at line 255 of file seq_map.hpp.
Referenced by CSeqMap_CI_SegmentInfo::GetRefPosition(), CSeqMap::HasZeroGapAt(), CSeqMap_CI_SegmentInfo::InRange(), CSeqMap::LoadSeq_data(), CSeqMap::SPosLessSegment::operator()(), CSeqMap::CSegment::operator=(), CSeqMap::SetRegionInChunk(), CSeqMap_CI_SegmentInfo::x_GetLevelRealEnd(), CSeqMap::x_GetSegmentLength(), CSeqMap_CI_SegmentInfo::x_Move(), CSeqMap::x_ResolveSegmentLength(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().
◆ m_Master ◆ m_MasterPos TSeqPos CSeqMapSwitchPoint::m_MasterPos ◆ m_MasterRange ◆ m_Mol [1/2] ◆ m_Mol [2/2] ◆ m_ObjType char CSeqMap::CSegment::m_ObjTypeDefinition at line 260 of file seq_map.hpp.
Referenced by CSeqMap::CSegment::IsSetData(), CSeqMap::CSegment::operator=(), CSeqMap::SetRegionInChunk(), CSeqMap::x_AddGap(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap::x_GetChunkToLoad(), CSeqMap::x_GetObject(), CSeqMap::x_GetSeq_data(), CSeqMap::x_GetSeq_literal(), CSeqMap::x_LoadObject(), CSeqMap::x_SetChunk(), CSeqMap::x_SetObject(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().
◆ m_Position atomic<TSeqPos> CSeqMap::CSegment::m_Position mutableDefinition at line 253 of file seq_map.hpp.
Referenced by CSeqMap_CI::CSeqMap_CI(), CSeqMap_CI_SegmentInfo::GetRefPosition(), CSeqMap::HasZeroGapAt(), CSeqMap_CI_SegmentInfo::InRange(), CSeqMap::InsertSegmentGap(), CSeqMap::LoadSeq_data(), CSeqMap::SPosLessSegment::operator()(), CSeqMap::CSegment::operator=(), CSeqMap::RemoveSegment(), CSeqMap::SetRegionInChunk(), CSeqMap::x_AddEnd(), CSeqMap::x_FindSegment(), CSeqMap::x_GetChunkToLoad(), CSeqMap_CI_SegmentInfo::x_GetLevelRealEnd(), CSeqMap_CI_SegmentInfo::x_GetLevelRealPos(), CSeqMap::x_LoadObject(), CSeqMap_CI_SegmentInfo::x_Move(), CSeqMap::x_ResolveSegmentPosition(), and CSeqMap::x_SetChanged().
◆ m_Randomizer ◆ m_RandomTable ◆ m_RefMinusStrand bool CSeqMap::CSegment::m_RefMinusStrand ◆ m_RefObjectDefinition at line 265 of file seq_map.hpp.
Referenced by CSeqMap::CSegment::operator=(), CSeqMap::SetRegionInChunk(), CSeqMap::x_AddGap(), CSeqMap::x_AddSegment(), CSeqMap::x_GetChunkToLoad(), CSeqMap::x_GetObject(), CSeqMap::x_GetSeq_data(), CSeqMap::x_GetSeq_literal(), CSeqMap::x_LoadObject(), CSeqMap::x_SetChunk(), CSeqMap::x_SetObject(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().
◆ m_RefPosition TSeqPos CSeqMap::CSegment::m_RefPosition ◆ m_Resolved atomic<size_t> CSeqMap::m_Resolved mutableprotected ◆ m_RightDifferences ◆ m_RightId ◆ m_RightMinusStrand bool CSeqMapSwitchPoint::m_RightMinusStrand ◆ m_RightPos TSeqPos CSeqMapSwitchPoint::m_RightPos ◆ m_Scope ◆ m_SegmentsDefinition at line 385 of file seq_map.hpp.
Referenced by CSeqMap::CountSegmentsOfType(), CSeqMap::CSeqMap(), CSeqMap::GetSegmentsCount(), CSeqMap::HasSegmentOfType(), CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::x_AddEnd(), CSeqMap::x_AddGap(), CSeqMap::x_AddSegment(), CSeqMap::x_FindSegment(), CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegment(), CSeqMap::x_GetSegmentPosition(), CSeqMap::x_ResolveSegmentPosition(), CSeqMap::x_SetSegment(), and CSeqMap::~CSeqMap().
◆ m_SegType char CSeqMap::CSegment::m_SegTypeDefinition at line 259 of file seq_map.hpp.
Referenced by CSeqMap::CreateSeqMapForSeq_loc(), CSeqMap::GetSeqMapForSeq_loc(), CSeqMap::HasZeroGapAt(), CSeqMap::CSegment::IsSetData(), CSeqMap::CSegment::operator=(), CSeqMap::RemoveSegment(), CSeqMap::SetRegionInChunk(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap_CI::x_Found(), CSeqMap::x_GetChunkToLoad(), CSeqMap::x_GetObject(), CSeqMap::x_GetRefSeqid(), CSeqMap::x_GetSeq_data(), CSeqMap::x_GetSubSeqMap(), CSeqMap::x_LoadObject(), CSeqMap_CI::x_Push(), CSeqMap_CI::x_RefTSEMatch(), CSeqMap::x_ResolveSegmentLength(), CSeqMap::x_SetChunk(), CSeqMap::x_SetObject(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), CSeqMap::x_SetSegmentRef(), and CSeqMap::x_SetSeq_data().
◆ m_SeqLength atomic<TSeqPos> CSeqMap::m_SeqLength mutableprotected ◆ m_SeqMap ◆ m_SeqMap_MtxDefinition at line 407 of file seq_map.hpp.
Referenced by CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::SetRegionInChunk(), CSeqMap::x_FindSegment(), CSeqMap::x_GetChunkToLoad(), CSeqMap::x_LoadObject(), CSeqMap::x_ResolveSegmentPosition(), CSeqMap::x_SetObject(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().
◆ m_Size ◆ m_Strand ◆ m_TSE ◆ m_UnknownLength bool CSeqMap::CSegment::m_UnknownLength ◆ CBioseq_Handle ◆ CBioseq_Info ◆ CSegment ◆ CSeqMap_CI ◆ CSeqMap_CI_SegmentInfo ◆ CSeqMap_SeqPoss friend class CSeqMap_SeqPoss friendDefinition at line 237 of file seq_map.hpp.
◆ CSeqVector_CI ◆ SPosLessSegmentRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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