src/objmgr/seq_map_switch.cpp File Reference

#include <ncbi_pch.hpp>
#include <objmgr/seq_map_switch.hpp>
#include <objmgr/seq_map.hpp>
#include <objmgr/seq_map_ci.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/impl/seq_align_mapper.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objects/seq/Seq_hist.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <algorithm>

Include dependency graph for seq_map_switch.cpp:

Go to the source code of this file.

Typedefs
typedef SMatchInfo	TMatch
typedef vector< SMatch >	TMatches
typedef pair< CSeq_id_Handle, CSeq_id_Handle >	TKey
typedef map< TKey, TMatches >	TMatchMap
typedef CSeqMapSwitchPoint::TDifferences	TDifferences
Functions
CNcbiOstream &	operator<< (CNcbiOstream &out, const SSeqPos &pos)
CRef< CSeqMapSwitchPoint >	x_GetSwitchPoint (const CBioseq_Handle &seq, SSeq_align_Info &info, const CSeqMap_CI &iter1, const CSeqMap_CI &iter2)
CSeqMapSwitchPoint::TInsertDelete	x_GetDifferences (const CSeqMapSwitchPoint::TDifferences &diff, TSeqPos offset, TSeqPos add)
CRef< CSeqMapSwitchPoint >	GetSwitchPoint (const CBioseq_Handle &seq, const CSeq_align &align)
TSeqMapSwitchPoints	GetAllSwitchPoints (const CBioseq_Handle &seq, const TSeqMapSwitchAligns &aligns)
TSeqMapSwitchPoints	GetAllSwitchPoints (const CBioseq_Handle &seq)
Variables
CSeq_id_Handle	id
TSeqPos	pos
bool	minus_strand
CBioseq_Handle	m_Master
set< CSeq_id_Handle >	m_SegmentIds
CConstRef< CSeq_align >	align
CSeq_id_Handle	id1
CRange< TSeqPos >	range1
CSeq_id_Handle	id2
CRange< TSeqPos >	range2
bool	same_strand
CConstRef< CSeq_align >	align
bool	skip
TSeqPos	m1
TSeqPos	m2
TMatchMap	match_map

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Typedef Documentation

typedef CSeqMapSwitchPoint::TDifferences TDifferences

Definition at line 302 of file seq_map_switch.cpp.

typedef pair<CSeq_id_Handle, CSeq_id_Handle> TKey

Definition at line 279 of file seq_map_switch.cpp.

typedef SMatchInfo TMatch

Definition at line 219 of file seq_map_switch.cpp.

typedef vector<SMatch> TMatches

Definition at line 278 of file seq_map_switch.cpp.

typedef map<TKey, TMatches> TMatchMap

Definition at line 280 of file seq_map_switch.cpp.

---

Function Documentation

TSeqMapSwitchPoints GetAllSwitchPoints (  const CBioseq_Handle &  seq  )

Definition at line 659 of file seq_map_switch.cpp. References GetAllSwitchPoints(), and CBioseq_Handle::GetInst_Hist().

TSeqMapSwitchPoints GetAllSwitchPoints (  const CBioseq_Handle &  seq, const TSeqMapSwitchAligns &  aligns )

Definition at line 631 of file seq_map_switch.cpp. References CSeqMap::begin(), CSeqMap::eSeqRef, CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CSeqMap_CI::GetType(), ITERATE, NCBI_THROW, and x_GetSwitchPoint().

CRef<CSeqMapSwitchPoint> GetSwitchPoint (  const CBioseq_Handle &  seq, const CSeq_align &  align )

Definition at line 597 of file seq_map_switch.cpp. References align, and NCBI_THROW.

CNcbiOstream& @0::operator<< (  CNcbiOstream &  out, const SSeqPos &  pos )  [static]

Definition at line 105 of file seq_map_switch.cpp. References pos.

CSeqMapSwitchPoint::TInsertDelete @0::x_GetDifferences (  const CSeqMapSwitchPoint::TDifferences &  diff, TSeqPos  offset, TSeqPos  add )  [static]

Definition at line 422 of file seq_map_switch.cpp. References map_checker< Container >::begin(), and map_checker< Container >::end(). Referenced by CSeqMapSwitchPoint::GetDifferences().

CRef<CSeqMapSwitchPoint> @0::x_GetSwitchPoint (  const CBioseq_Handle &  seq, SSeq_align_Info &  info, const CSeqMap_CI &  iter1, const CSeqMap_CI &  iter2 )  [static]

Definition at line 383 of file seq_map_switch.cpp. References _ASSERT, eEnd, eStart, CSeqMap_CI::GetEndPosition(), CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefSeqid(), CSeqMapSwitchPoint::m_ExactMasterRange, CSeqMapSwitchPoint::m_FirstAlign, CSeqMapSwitchPoint::m_LeftDifferences, CSeqMapSwitchPoint::m_LeftId, CSeqMapSwitchPoint::m_LeftMinusStrand, CSeqMapSwitchPoint::m_LeftPos, CSeqMapSwitchPoint::m_Master, CSeqMapSwitchPoint::m_MasterPos, CSeqMapSwitchPoint::m_MasterRange, CSeqMapSwitchPoint::m_RightDifferences, CSeqMapSwitchPoint::m_RightId, CSeqMapSwitchPoint::m_RightMinusStrand, CSeqMapSwitchPoint::m_RightPos, pos, and COpenRange< Position >::SetFrom(). Referenced by GetAllSwitchPoints().

---

Variable Documentation

CConstRef<CSeq_align> align

Definition at line 203 of file seq_map_switch.cpp.

CConstRef<CSeq_align> align

Definition at line 175 of file seq_map_switch.cpp. Referenced by CObjectIndex::Add(), CAlignmentSmear::AddAlignments(), CDensityMap< CntType >::AddAlignments(), CSelectionEvent::AddObjectSelection(), CScoreBuilder::AddScore(), CFlFrame::align(), BlastCompo_AlignmentNew(), BlastCompo_AlignmentsFree(), BOOST_AUTO_TEST_CASE(), CBox::CBox(), CChain::CChain(), CFlatfileTCRenderer::CFlatfileTCRenderer(), CChain::ClipToCompleteAlignment(), CSeqScores::ConstructSequenceAndMaps(), Convert_Seq_align_ProjectItem(), Convert_Seq_align_Seq_annot(), Convert_Seq_align_Seq_id(), Convert_Seq_align_Seq_loc_Basic(), Convert_Seq_align_Seq_loc_Coalesced(), Convert_Seq_align_set_ProjectItem(), Convert_Seq_align_set_Seq_align(), Convert_Seq_align_set_Seq_annot(), Convert_Seq_align_set_Seq_loc(), Convert_Seq_entry_Seq_align(), Convert_Seq_loc_Seq_align(), ConvertToPairwise(), CPluginArgFormTitle::CPluginArgFormTitle(), CreateAlignRow(), CreateSparseAlign(), CSeq_align_Mapper::CreateSubAlign(), CSeq_align_Mapper_Base::CreateSubAlign(), CSeq_align_Mapper_Base::CSeq_align_Mapper_Base(), CSeq_hist_SplitInfo::CSeq_hist_SplitInfo(), CSeqScores::CSeqScores(), CSerialBrowserTree::CSerialBrowserTree(), CStatusBar::CStatusBar(), CTaskManagerStatusBarGadget::CTaskManagerStatusBarGadget(), CGradientPanel::draw(), CTaskManagerStatusBarGadget::draw(), CGeneModel::Extend(), CSeq_annot_Finder::Find(), CScoreBuilder::GetAlignLength(), CObjectIndex::GetAligns(), CScoreBuilder::GetBlastBitScore(), CScoreBuilder::GetBlastEValue(), CScoreBuilder::GetBlastScore(), GetDDSetFromSeqAlign(), CShowBlastDeflineTest::GetDeflineInfo(), CScoreBuilder::GetGapCount(), CScoreBuilder::GetIdentityCount(), CSeq_align_setHandler::GetLabel(), CSeq_alignHandler::GetLabel(), CAnnotObject_Info::GetMaps(), CObjectIndex::GetMatches(), CScoreBuilder::GetMismatchCount(), CScoreBuilder::GetPercentCoverage(), CScoreBuilder::GetPercentIdentity(), GetSwitchPoint(), CDefaultTCRenderer::GetTCRendererWidget(), CAlignGroup::GroupBySeqIds(), CAlignGroup::GroupBySequenceType(), CAlignGroup::GroupByStrand(), CObjectIndex::HasMatches(), CSparseMultiDataSource::Init(), AlignmentCollection::IsNonOverlapping(), CSeqGraphicPane::LHH_GetLegend(), MapPositionToChild(), MapPositionToMaster(), SCigarAlignment::operator()(), MarkupTrustedGenes::operator()(), MarkupCappedEst::operator()(), DoNotBelieveFrameShiftsWithoutCdsEvidence::operator()(), DoNotBelieveShortPolyATail::operator()(), TrimAlignment::operator()(), ProjectCDS::operator()(), OverlapsSameAccessionAlignment::operator()(), operator>>(), CValidError_base::PostErr(), CValidError_imp::PostErr(), RemapAlignToLoc(), CObjectIndex::Remove(), RestoreModel(), RestoreModelFromInternalGnomonFeature(), RestoreModelFromPublicMrnaFeature(), CChain::RestoreReasonableConfirmedStart(), CGeneModelDemoApp::Run(), s_Align2Annot(), s_AlignmentCopy(), s_AlignmentsAreSorted(), s_CheckTraceMateAlign(), s_CountSegments(), s_ExtractSeqId(), s_GetAlignmentContent(), s_GetAlignmentLength(), s_GetAlignmentTooltip(), s_GetAlignmentType(), s_GetCountIdentityMismatch(), s_GetCoveredBases(), s_GetGapCount(), s_GetPercentCoverage(), s_GetPercentIdentity(), s_GetSubjectComposition(), s_GetSubjectId(), s_GetText(), s_GetText_GenericAlign(), s_GetText_PairwiseAlign(), s_HSPListFromDistinctAlignments(), s_IsContained(), s_preliminaryTestNearIdentical(), s_Seq_align_Seq_loc(), s_SequenceGetRange(), s_SequenceGetTranslatedRange(), s_TestNearIdentical(), s_WindowInfoJoin(), s_WindowInfoNew(), s_WindowsFromProteinAligns(), s_WindowsFromTranslatedAligns(), s_WithDistinctEnds(), PssmScorer::score(), SelectCompartmentsHits(), CHitMatrixDataSource::SelectIds(), AnnotObjTrait< CSeq_align >::Set(), CDefaultTCRenderer::SetAlign(), SetAlignedResiduesOnSequence(), CAnnotMapping_Info::SetMappedSeq_align(), bm::sse2_bit_count(), bm::sse2_bit_count_op(), TextOutAligned(), TrimAlignment::TrimCodingExonLeft(), TrimAlignment::TrimCodingExonRight(), TrimAlignment::TrimProtein(), TrimAlignment::TrimTranscript(), CValidError_align::ValidateSeqAlign(), CVecscreenTest::VecscreenDisplay(), CDefaultPolicy::x_CalcAlignHeight(), CPhrap_Contig::x_CreateAlignAll(), CPhrap_Contig::x_CreateAlignOptimized(), CPhrap_Contig::x_CreateAlignPairs(), CHitMatrixDataSource::x_CreateIds(), CSeqGraphicWidget::x_CreatePopupMenu(), CPhrap_Contig::x_CreateSeq_align(), CDefaultPolicy::x_DrawAlignment(), CTracebackSearchTestFixture::x_FindUsedGis(), CHitMatrixDataSource::x_GetAlignedSeqIds(), CValidError_align::x_GetIds(), CAlnMultiDSBuilder::x_GetLinearAlignments(), CDefaultPolicy::x_GetRowHeight(), CDefaultPolicy::x_GetTitle(), CSeq_align_Mapper_Base::x_Init(), CSeqGraphicJob::x_LoadFeatProducts(), CGFFReader::x_ParseAlignRecord(), CGFFReader::x_PlaceAlignment(), CAnnotObject_Info::x_ProcessAlign(), CRegionMap::x_Roundup(), CSplitDataLoader::x_SplitAligns(), CHitMatrixDataSource::x_TestAndSelectAligns(), CValidError_align::x_ValidateAlignPercentIdentity(), CValidError_align::x_ValidateDendiag(), CValidError_align::x_ValidateDenseg(), CValidError_align::x_ValidateDim(), CValidError_align::x_ValidateFastaLike(), CValidError_align::x_ValidatePacked(), CValidError_align::x_ValidateSegmentGap(), CValidError_align::x_ValidateSeqId(), CValidError_align::x_ValidateSeqLength(), CValidError_align::x_ValidateStd(), and CValidError_align::x_ValidateStrand().

CSeq_id_Handle id

Definition at line 56 of file seq_map_switch.cpp. Referenced by AascanTestFixture::AascanTestFixture(), CSeqsRange::Add(), CSplitBlob::AddChunk(), CBioseq_Info::AddId(), SAlignment_Segment::AddRow(), CTaxNRCriteria::Apply(), CObjectOStreamXml::BeginClassMember(), BOOST_AUTO_TEST_CASE(), BuildGoodSeq(), CBioseq::CBioseq(), CComponentSearchJob::CComponentSearchJob(), CFeatureSearchJob::CFeatureSearchJob(), CEditAction_UpdateIds::ChangeId(), ChangeSeqLocId(), CheckDuplicates(), CEnumDataType::CheckValue(), CSeqIdDictionary::CheckWord(), CObjectIndex::Clear(), bm::combine_and_sorted(), CTSE_Split_Info::ContainsBioseq(), CTSE_Chunk_Info::ContainsBioseq(), CTSE_ScopeInfo::ContainsBioseq(), Convert_Seq_feat_Seq_loc_dbxref_Loc(), ASNDataManager::ConvertMimeDataToCDD(), CInsertAnnotHookId::CopyClassMember(), CEntrezDB::CreateAnnot_Genome(), CEntrezDB::CreateAnnot_Nuc_Prot(), CBlastBioseqMaker::CreateBioseqFromId(), CAlnVec::CreateConsensus(), CEnumDataType::CreateDefault(), XSDParser::CreateEntityId(), CEntrezDB::CreateId_Nuc_Prot(), XSDParser::CreateTypeDefinition(), WSDLParser::CreateWsdlName(), CSequenceSearchJob::CSequenceSearchJob(), bm::iterator_deserializer< BV, SerialIterator >::deserialize(), CAddBioseqChecker::Do(), CRemoveIdChecker::Do(), CIDs::Encode(), CHitSeqRowId::Equals(), CHitSeqId::Equals(), CCdCore::EraseStructureEvidence(), CID1Client::FetchEntry(), FillSets(), CDense_seg::FillUnaligned(), CTaxon1::FindTaxIdByName(), ForEach(), CFtableFormatter::FormatFeatHeader(), CFastaReader::GenerateID(), GenerateSparseSeg(), CBioseq_Handle::GetAccessSeq_id_Handle(), CLDS_Object::GetAnnotInfo(), CSimpleOM::GetBioseqHandle(), CScope_Impl::GetBioseqHandle(), GetCDDPssmIdFromSeqId(), CThreadSystemID::GetCurrent(), CEnumDataType::GetDefaultString(), oligofar::CSeqIds::CSeqDef::GetFullIdString(), CSeq_id_Handle::GetHandle(), GetLabel(), CHitMatrixDataSource::GetLabel(), oligofar::CSeqIds::GetOrdById(), GetProductLabel(), CBioseq_Handle::GetRangeSeq_loc(), CTraceChromatogramLoader::GetRecords(), CCddDataLoader::GetRecords(), CViewGraphic::GetSearchLoc(), AalookupTestFixture::GetSeqBlk(), CTSE_Info::GetSeqMatch(), CSeq_loc_mix::GetStrand(), CPacked_seqint::GetStrand(), GetTitle(), CGBReaderRequestResult::GetTSE_LoadLock(), CGBReaderRequestResult::GetTSE_LoadLockIfLoaded(), CSeq_loc_Conversion::GoodSrcId(), CMappingRange::GoodSrcId(), CTraceDataProxy::HasData(), CBioseq_Info::HasId(), inflateSetDictionary(), CAlignSeqTableModel::Init(), CSafeStaticPtr_Base::Init_Lock(), CWinMaskConfig::CIdSet_SeqId::insert(), CBlastBioseqMaker::IsProtein(), CTraceDataProxy::LoadData(), CId1FetchApp::LookUpFastaSeqID(), CId1FetchApp::LookUpFlatSeqID(), CIdMapper::Map(), CCdAnnotationInfo::MappedToSlaveString(), CAnnotationASN1::CImplementationData::model2spliced_seq_align(), CPrefetchTokenOld_Impl::NextBioseqHandle(), CFileDBEngine::NotifyIdChanged(), NS_DecodeBitVector(), RpsTestFixture::NuclSearch(), CBlobIdKey::operator!=(), CPsiBlastAlignmentProcessor::operator()(), CBlob_id::operator<(), CAlnSeqId::operator<(), CBlobIdKey::operator<(), operator<<(), CBlobIdKey::operator==(), CMaskWriterBlastDbMaskInfo::Print(), CSplitCacheApp::Process(), CSplitCacheApp::ProcessGi(), PSSMWrapper::PSSMWrapper(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CConversionApp::Read(), CReadBlastApp::ReadBlast(), CBlastInputReader::ReadOneSeq(), oligofar::CSeqIds::Register(), CBioseq_Info::RemoveId(), RetrieveGi555WithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), RetrievePartsOfLargeChromosome(), CDemoApp::Run(), CGi2TaxIdApp::Run(), CTestProtProd_EntrezNeighbors::RunTest(), s_AddBioseqToBioseq(), s_AddPartToSegmentedBioseq(), s_BlastHSPBestHitFinal(), s_BlastHSPCullingFinal(), s_ConvertToBlastQueries(), s_DumpSequence(), s_FindLeafDistances(), s_GetAlignedSeqGi(), s_GetId(), s_GetNameForBioseq(), s_GetNewIdHandle(), s_GetTargetId(), s_IsNcOrNt(), s_ParseFastaDefline(), s_ScoreForDBSource(), s_SeqDB_ParseSeqIDs(), s_TestFastaRoundTrip(), SeqLocToBioseq(), CTSE_Info_Object::SetBioObjectId(), CStlOneArgTemplate::SetDataId(), CPhyTreeNode::SetFeature(), CAlignShadow::SetId(), CStlTwoArgsTemplate::SetKeyId(), CAlignShadow::SetQueryId(), CDisplaySeqalign::SetSubjectMasks(), CAlignShadow::SetSubjId(), TestFixture::SetUpQuery(), CStlTwoArgsTemplate::SetValueId(), tds_process_compute_095(), TestDataNotFound(), CSampleEditSaver::UpdateSeq(), CSeqTableLocColumns::UpdateSeq_loc(), CValidError_bioseq::ValidateIDSetAgainstDb(), CBuildDatabase::x_AddRemoteSequences(), CSeqDBVol::x_CheckVersions(), CStudyLoader::x_CreateSeqFtable(), CStudyLoader::x_CreateSeqGraph(), CComponentSearchJob::x_DoSearch(), CTSE_Split_Info::x_FindChunk(), CSeq_id_PDB_Tree::x_FindInfo(), CScope_Impl::x_FindSeq_id_Info(), CSeq_id_Textseq_Tree::x_FindStrInfo(), CDBSourceItem::x_FormatDBSourceID(), CAlnGraphic::x_GetAlnInfo(), CSeq_align_Mapper_Base::x_GetDstDendiag(), CSeq_align_Mapper_Base::x_GetDstStd(), CSeq_loc_Mapper_Base::x_GetMappedRanges(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CPromote::x_GetProductId(), CTSE_Split_Info::x_GetRecords(), CScope_Impl::x_GetSeq_id_Info(), CAltValidator::x_GetTaxonSpecies(), CGBenchApp::x_HandleArgs(), CGBenchApp::x_HandleRemote(), CTSE_Info::x_IndexAnnotTSE(), CDataSource::x_IndexTSE(), CSeqGraphicJob::x_LoadSNPMarkers(), CSnpViewUI::x_OnButtonSeqLoad(), CSnpViewUI::x_OnButtonTableLoad(), CSeqTextDemoUI::x_OnLoadAccession(), CSeqGraphicDemoUI::x_OnLoadAccession(), CHitMatrixDemoUI::x_OnLoadAccession(), CMultiDemoUI::x_OnLoadAccession(), CCrossAlnDemoUI::x_OnLoadAccession(), CSeq_loc_Mapper_Base::x_PushSourceRange(), x_RangesToSeq_loc(), CCompartApp::x_ReadSeqLens(), CFastaReader::x_ReadSeqsToAlign(), CTSE_Info::x_ResetBioseqId(), CGFFReader::x_ResolveID(), CBuildDatabase::x_ResolveRemoteId(), CGFFReader::x_ResolveSeqName(), CValidError_feat::x_SeqIdToGiNumber(), CReaderBase::x_SetBrowserRegion(), CMicroArrayReader::x_SetFeatureLocation(), CTSE_Info::x_SetIdObjects(), CSeqMap::x_SetSegmentRef(), x_TestGetFilteredQueryRegions(), CSequenceDataTester::x_TestSingleNucleotide_Local(), CSequenceDataTester::x_TestSingleProtein_Local(), CSeq_id_PDB_Tree::x_Unindex(), CSeq_id_Patent_Tree::x_Unindex(), CSeq_id_Giim_Tree::x_Unindex(), CSeq_id_Local_Tree::x_Unindex(), CTSE_Info::x_UnindexAnnotTSE(), CTSE_ScopeInfo::x_UnindexBioseq(), CSeq_loc::x_UpdateId(), CResolveIdDlg::x_UpdateIds(), CSeq_loc::x_UpdateTotalRange(), CValidError_align::x_ValidateSegmentGap(), CValidError_align::x_ValidateSeqLength(), and CValidError_align::x_ValidateStrand().

CSeq_id_Handle id1

Definition at line 176 of file seq_map_switch.cpp. Referenced by CIdMapper::AddMapping(), BOOST_AUTO_TEST_CASE(), CAlnMix::ChooseSeqId(), DoSearchWordSize4(), FIdEqual(), IsSameBioseq(), SProjectItem_Less::operator()(), CAlnMixSequences::SSeqIds::operator()(), CDemoContigAssemblyApp::Run(), s_CanAdd(), s_Compare(), s_OOFBlastHSP2SeqAlign(), s_PercentBioseqMatch(), SameCDAccession(), CSplignFormatter::SetSeqIds(), CValidError_imp::ValidateSeqLocIds(), CBlastTabular::x_Deserialize(), CDefaultPolicy::x_DrawRuler(), and CSeq_id_Textseq_Tree::x_Equals().

CSeq_id_Handle id2

Definition at line 178 of file seq_map_switch.cpp. Referenced by CIdMapper::AddMapping(), BOOST_AUTO_TEST_CASE(), CAlnMix::ChooseSeqId(), CWriteDB_Impl::CreateColumn(), DoSearchWordSize4(), FIdEqual(), CFlatFileGenerator::Generate(), IsSameBioseq(), CBlobId::LessByTypeId(), SProjectItem_Less::operator()(), CAlnMixSequences::SSeqIds::operator()(), CObject_id::operator<(), CDemoContigAssemblyApp::Run(), s_CanAdd(), s_Compare(), s_OOFBlastHSP2SeqAlign(), s_PercentBioseqMatch(), s_TestFastaRoundTrip(), SameCDAccession(), CSplignFormatter::SetSeqIds(), CValidError_imp::ValidateSeqLocIds(), CBlastTabular::x_Deserialize(), CDefaultPolicy::x_DrawRuler(), CSeq_id_Textseq_Tree::x_Equals(), and CSeq_id_PDB_Tree::x_Unindex().

TSeqPos m1

Definition at line 205 of file seq_map_switch.cpp. Referenced by BOOST_AUTO_TEST_CASE(), dbmny4add(), dbmny4cmp(), dbmny4divide(), dbmny4mul(), dbmny4sub(), dbmnyadd(), dbmnycmp(), dbmnydivide(), dbmnymul(), dbmnysub(), CPathHook::Match(), Matrix::Matrix(), operator *(), operator *=(), operator!=(), operator+(), operator+=(), operator-(), operator-=(), operator/(), operator==(), CSRSearch::reportResults(), bm::sse2_bit_count(), and bm::sse2_bit_count_op().

TSeqPos m2

Definition at line 205 of file seq_map_switch.cpp. Referenced by BOOST_AUTO_TEST_CASE(), dbmny4add(), dbmny4cmp(), dbmny4divide(), dbmny4mul(), dbmny4sub(), dbmnyadd(), dbmnycmp(), dbmnydivide(), dbmnymul(), dbmnysub(), Matrix::Matrix(), operator *(), operator+(), operator-(), CSRSearch::reportResults(), bm::sse2_bit_count(), and bm::sse2_bit_count_op().

CBioseq_Handle m_Master

Definition at line 113 of file seq_map_switch.cpp. Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CBioseqContext::GetMaster(), and CSeqMapSwitchPoint::operator<().

set<CSeq_id_Handle> m_SegmentIds

Definition at line 114 of file seq_map_switch.cpp.

TMatchMap match_map

Definition at line 300 of file seq_map_switch.cpp. Referenced by CDataSource_ScopeInfo::GetBlobs(), and CDataSource::GetBlobs().

bool minus_strand

Definition at line 58 of file seq_map_switch.cpp.

TSeqPos pos

Definition at line 57 of file seq_map_switch.cpp. Referenced by hashtable< _Val, _Key, _HF, _ExK, _EqK, _All >::_M_next_size(), _PSICheckSequenceWeights(), _PSIComputeSequenceWeights(), _PSISpreadGapWeights(), CSeq_locFormatter::Add(), CCgiCookies::Add(), CWorkspaceWindow::AddClient(), CWindowManager::AddClient(), CWindowManager::AddClientToDock(), CLoaderStrFormatter::AddGIPrefix(), BlockIntersector::addOneAlignment(), AddPeriod(), SAccGuide::AddRule(), CSystemPath::AddToPath(), CDB_Stream::Assign(), CBlobSplitterImpl::AttachToSkeleton(), CShutdownProcessor::Authenticate(), CProSplignOutputOptionsExt::BackCheck(), tree< T, tree_node_allocator >::begin(), tree< T, tree_node_allocator >::begin_fixed(), impl::CDBBindedParams::Bind(), BOOST_AUTO_TEST_CASE(), CBookmarkMgrDlg::CBookmarkMgrDlg(), CCgiEntryReaderContext::CCgiEntryReaderContext(), CDBUriConnParams::CDBUriConnParams(), CDiagStrPathMatcher::CDiagStrPathMatcher(), AbstractLexer::Char(), CTextUtil::CleanJournalTitle(), CleanStringList(), CChain::ClipToCompleteAlignment(), CMessageDlg::CMessageDlg(), CNamespace::CNamespace(), CLocMapper_Default::CollapseRanges(), CollectProteinFrequences(), XStr::CompareCase(), CCgiStatistics::Compose_Entries(), CId2Compressor::CompressChunk(), CDirEntry::ConcatPathEx(), ContainsSgml(), CPepXML::ConvertModifications(), CObjectOStream::CopyClassSequential(), oligofar::COutputFormatter::CoTranslate(), CGBenchWorkspaceWindow::CreateNewView(), CreateSubmenuByPath(), CGBenchWorkspaceWindow::CreateView(), CSymbolGuard::CSymbolGuard(), CWinMaskCountsGenerator::CWinMaskCountsGenerator(), CSubSource::DateFromCollectionDate(), ddAcumAliCord(), ddAlignInfo(), ddRecompose(), CDbapiSampleApp::DeleteLostTables(), CDirEntry::DeleteTrailingPathSeparator(), Denseg2DenseDiagList(), tree< T, tree_node_allocator >::depth(), CRemoteAppRequestSB_Impl::Deserialize(), CDistMethods::Divergence(), CSeqMaskerOstatOpt::doSetParam(), CSeqMaskerOstatBin::doSetParam(), CTestViewable::draw(), CTestScrollable::draw(), tree< T, tree_node_allocator >::end(), tree< T, tree_node_allocator >::end_fixed(), CRegexp::Escape(), CScannerFunctorEQ::Eval(), ExcludeBadExons(), CPatternStats::ExpandPattern(), CFormattingArgs::ExtractAlgorithmOptions(), ExtractReaderContents(), AbstractLexer::FillChar(), CWinMaskConfig::CIdSet_TextMatch::find(), array_set< T, Cmp >::find(), array_map< K, V, Cmp, kCapacityIncrement >::find(), CCgiEntry::find(), CCgiEntry::find_first_of(), find_match(), python::CStmtStr::find_named(), python::CStmtStr::find_numeric(), CSymDustMasker::triplets::find_perfect(), array_set< T, Cmp >::find_pos(), array_map< K, V, Cmp, kCapacityIncrement >::find_pos(), python::CStmtStr::find_TSQL(), FindAllCodonInstances(), CIStreamBuffer::FindChar(), FindFirstStart(), FindForwardOrfs(), NStr::FindNoCase(), FindPolyA(), CBDB_ExtBlobStore< TBV >::Flush(), CAgpErr::FormatMessage(), CProSplignOutputOptionsExt::ForwCheck(), CSnpMarkers::FromSeqAnnot(), CContElemConverter< CCgiEntry >::FromString(), impl::g_SubstituteParam(), oligofar::CFaDiceApp::GeneratePair(), oligofar::CFaDiceApp::GenerateRead(), bm::bvector_mini< A >::get_first(), get_next_tok(), GetAlignmentColumnsForCD(), StyleManager::GetAtomStyle(), CScope_Impl::GetBioseqHandles(), BMAUtils::GetCharacterAndIndexForColumn(), CBlockedAlignmentEditor::GetCharacterForColumn(), CWMTabControl::GetChild(), CWMSplitter::GetChild(), CWMFrameWindow::GetChild(), CWMDockContainer::GetChild(), CViewBase::GetClientLabel(), CAlnVec::GetColumnVector(), CFastaReader::GetCurrentPos(), GetDefaultLogLocation(), CCgiApplication::GetDefaultLogPath(), CSplitter::GetHeights(), CWinMaskSeqTitle::GetId(), CSeqportUtil_implementation::GetIndex(), GetIntergenicSpacerClauseList(), GetItemLabelFromPath(), CQueryDataPerChunk::GetLastChunk(), AlignmentCollection::GetLowerBound(), CPluginHandle_Impl::GetMenuPath(), CFastaBioseqSource::GetNext(), CWindowManager::GetPopupItems(), CQueryDataPerChunk::GetQueryLength(), SNetCacheAPIImpl::GetReadStream(), CAlnVec::GetResidue(), CSeqVector_CI::GetSeqData(), CBlockedAlignmentEditor::GetSeqIndexForColumn(), CAlnMap::GetSeqPosFromAlnPos(), CAlnMap::GetSeqPosFromSeqPos(), CDense_seg::GetSeqStart(), CDense_seg::GetSeqStop(), CAutoDefModifierCombo::GetSourceDescriptionString(), CSystemPath::GetStdPath(), IBlastSeqVector::GetStrandData(), CFastaIOWrapper::GetSubstring(), COrgRefCache::GetSubtypeFromName(), CSeqGraphicRenderer::GetTooltip(), CImageIO::GetTypeFromFileName(), CCodeGenerator::GetTypes(), CPluginHandle_Impl::GetUIName(), AlignmentCollection::GetUpperBound(), CRegistryData_File::GetValue(), CAlnVec::GetWholeAlnSeqString(), CSplitter::GetWidths(), CTextUtil::GetWordFrequencies(), TaxTreeData::growAndInsertLineage(), CFastIScore::Init(), CNSeq::Init(), CSeqportUtil_implementation::InitFastIupacnaNcbi2na(), CSeqportUtil_implementation::InitFastIupacnaNcbi4na(), CDiscreteDistribution::InitFromParameter(), impl::CRowInfo_SP_SQL_Server::Initialize(), CWMTabControl::Insert(), CSeqMap::InsertSegmentGap(), CGBenchWindowManager::InstantiateLayout(), NStr::Int8ToString(), NStr::IntToString(), CWMTabControl::IsAvailable(), CWMSplitter::IsAvailable(), CWMFrameWindow::IsAvailable(), CWMDockContainer::IsAvailable(), CRefArgs::IsListedHost(), IsLocalPath(), CWMTabControl::IsOccupied(), CWMSplitter::IsOccupied(), CWMFrameWindow::IsOccupied(), CWMDockContainer::IsOccupied(), CBlockedAlignmentEditor::IsResidueAtIndexOnAllRows(), CValidError_imp::IsSerialNumberInComment(), IsSpName(), CCountries::IsValid(), LaunchWebPage(), CWindowManager::LayoutToUserObject(), CGBProjectHandle::Load(), CId1FetchApp::LookUpFlatSeqID(), make_server(), MakeSeqLocFromDD(), CWiggleTrack::MakeTable(), CWig2tableApplication::MakeTable(), BlockModel::mask(), CDiagStrPathMatcher::Match(), CVariant::MoveTo(), NcbiGetline(), CAlignedFeatureGraph::NeedTooltip(), NultriposToProduct_pos(), tree< T, tree_node_allocator >::iterator_base::number_of_children(), tree< T, tree_node_allocator >::number_of_children(), tree< T, tree_node_allocator >::number_of_siblings(), CWindowManager::OnContainerCommand(), CGBenchWindowManager::OnContainerCommand(), CWindowManager::OnContainerUpdateCommand(), CGBenchWindowManager::OnContainerUpdateCommand(), CWindowManager::OnInsertSplitter(), CWindowManager::OnMoveToFrame(), CTestScrollable::OnScroll(), CMapControl::OnScroll(), CLDS_CoreObjectsReader::OnTopObjectFoundPre(), CTextPrinter::operator()(), ProjectCDS::operator()(), operator<<(), CSnpMarkers::SMarkerInfo::operator==(), CFastaReader::ParseDefLine(), SDiagMessage::ParseMessage(), CFastaReader::ParseRange(), CDBUriConnParams::ParseServer(), CDBUriConnParams::ParseSlash(), CIStreamBuffer::PeekFindChar(), PluginInfoFromRegistry(), CAutoDefFeatureClause_Base::PluralizeInterval(), CAlnVecPrinter::PopsetStyle(), oligofar::CQueryHash::PopulateDeletions(), oligofar::CQueryHash::PopulateInsertions(), CMzXML2hdf5Application::ProcessFiles(), CBDB_ResultStore< TBV >::CResultStoreEnumerator::ProcessNewFetch(), CGBenchIndexCgi::ProcessRequest(), CSimpleDictionary::Read(), Ctbl_seg::Read(), CBDB_ExtBlobStore< TBV >::ReadBlob(), CObjectIStream::ReadClassSequential(), CImageIO::ReadImageInfo(), CLDS_CoreObjectsReader::ReadObject(), CWMTabControl::Remove(), CWMSplitter::Remove(), CWMFrameWindow::Remove(), CWMDockContainer::Remove(), BlockIntersector::removeOneAlignment(), CSeqMap::RemoveSegment(), RemoveSpaceBeforeAndAfterColon(), RemoveWhiteSpace(), CSeqMarkHandler::Render(), CBookmarksHandler::Render(), tree< T, tree_node_allocator >::reparent(), python::RetrieveStatementType(), CSnpFilterJob::Run(), CGBenchMonitorApp::Run(), CPkl2hdf5Application::Run(), CGi2TaxIdApp::Run(), CTestTranscript_PolyA::RunTest(), s_AfterPrefix(), s_AssignEntryValue(), s_BadCharsInAuthorName(), s_CheckGZipHeader(), s_Code_break(), s_ConvertComment(), s_CreateHTMLPage(), s_DescribeClones(), s_ExtractLast(), s_ExtractSatelliteFromComment(), s_FillCdsStartPosition(), s_FillContigMBTable(), s_FillDiscMBTable(), s_FindParam(), s_Fingerprint_Dense_diag(), s_Fingerprint_Dense_seg(), s_Fingerprint_Packed_seg(), s_Fingerprint_Packed_seqpnt(), s_Fingerprint_Seq_point(), s_Fingerprint_Sparse_align(), s_GetAbsoluteContextLength(), s_GetDigits(), s_IsValidPrimerSequence(), s_Length(), s_NewGapItem(), s_NofTokens(), s_ParseSubNodes(), s_ParseVersion(), s_PHIGetExtraLongPattern(), s_ReplaceArg(), s_SeqDB_ParseSeqIDs(), s_SeqDBMapNA2ToNA8(), s_SplitName(), s_StringHasPMID(), s_StringToOrgMod(), s_StringToSubSource(), s_TestFastaRoundTrip(), s_tRNAClauseFromNote(), s_URLDecode(), s_ValidateFile(), SCigarAlignment::SCigarAlignment(), CBoyerMooreMatcher::Search(), SSnpFilter::SerializeFrom(), impl::CDBBindedParams::Set(), CAlnMap::SetAnchor(), COrgRefCache::SetBinomialName(), CSeqVector_CI::SetCoding(), CSplitter::SetHeights(), CDataType::SetParentClassTo(), CSeqVector_CI::SetRandomizeAmbiguities(), CSRSearch_Impl< index_t >::setResults4Idx(), python::CStmtStr::SetStr(), CSeqVector_CI::SetStrand(), CDDAnnotateDialog::SetupGUIControls(), CUrl::SetUrl(), CSplitter::SetWidths(), CObjectIStream::SkipClassSequential(), CIStreamBuffer::SkipSpaces(), CWinMaskConfig::CIdSet_TextMatch::split(), CDirEntry::SplitPath(), CDirEntry::SplitPathEx(), CCachedSequence::SplitSeqData(), NStr::StringToDoubleEx(), NStr::StringToInt8(), CSeqDBIsam::StringToOids(), NStr::StringToUInt8(), NStr::StringToUInt8_DataSize(), CHTMLHelper::StripSpecialChars(), CHTMLHelper::StripTags(), CId2Compressor::sx_Append(), sx_FetchNextItem(), tds5_fix_dot_query(), tds_money_to_string(), test_gzio(), CFormatGuess::TestFormatSnpMarkers(), CGlBitmapFont::TextOut(), CWMTabControlDescr::ToUserObject(), CWMSplitterDescr::ToUserObject(), TracebackAlignment(), TrimInternalSemicolons(), NStr::UInt8ToString(), NStr::UIntToString(), CRegistryItemPanel::Update(), CScrollGroup::UpdateScrollBars(), CDB_Numeric::Value(), CCountries::WasValid(), CRegexp::WildcardToRegexp(), WrapText(), CDefaultLayoutPolicy::x_AddAssnStudyFromGraph(), CWindowManager::x_AddClient(), CSeqMap::x_AddEnd(), CAutoDefModifierCombo::x_AddOrgModString(), CAutoDefModifierCombo::x_AddSubsourceString(), CStreamLineReader::x_AdvanceEOLSimple(), CQueueDataBase::x_AllocateQueue(), x_Append4To4(), CScoringJob::x_CalculateAlignmentScores(), CCachedSeqDataForRemote::x_CalculateNumberOfSlices(), CSeq_loc::x_CalculateTotalRangeCheckId(), CCgiCookie::x_CheckField(), CNetScheduleHandler::x_CheckVersion(), CCleanup_imp::x_CleanupConsSplice(), CAutoDefModifierCombo::x_CleanUpTaxName(), CWindowManager::x_Close(), CFastaReader::x_CloseGap(), CSplitter::x_Create(), CGBenchWorkspaceWindow::x_CreateManageDataSourcesSubmenu(), CGBenchWorkspaceWindow::x_CreateNewView(), CWindowManager::x_CreateRootContainers(), CStudyLoader::x_CreateSeqAnnots(), CStudyLoader::x_CreateSeqFtable(), CDeflineGenerator::x_DescribeClones(), CSplitter::x_DoDistributeEvenly(), CMenu::x_DrawItemText(), CDefaultPolicy::x_DrawSwitchPoints(), CMapItem::x_DrawText(), CTreeBrowser::x_EscapeSlashes(), CViewAsn::x_Find(), CAlnMap::x_FindClosestSeqPos(), x_FindRSite(), CViewAsn::x_FindSpan(), CViewAsn::x_FindSpanNest(), CCgiEntry::x_GetCharset(), CSeqMarkHandler::x_GetMarkRect(), CBookmarksHandler::x_GetMarkRect(), CSequenceSearchJob::x_GetMatches(), CWindowManager::x_GetMoveFromFrameMenu(), CWindowManager::x_GetMoveHereMenu(), CWig2tableApplication::x_GetParamValue(), CRuler::x_GetPositionLabel(), x_GetSwitchPoint(), CNcbiTestApplication::x_GetTrimmedTestName(), CListPanel::x_HandleColHeaderClick(), CSplitter::x_HitTest(), CSplitter::x_HitTestSeparator(), CGlTexture::x_InitTexObj(), CWindowManager::x_InsertClient(), CWindowManager::x_InsertSplitter(), oligofar::CSeqScanner::x_MainLoop(), CWindowManager::x_MoveClientToTopLevel(), CWindowManager::x_MoveInContainer(), CSplitter::x_MoveSeparator(), CSeqVector_CI::x_NextCacheSeg(), CRegistryDlg::x_NodeToKey(), CFilterDlg::x_OnChangeColumn(), CFilterDlg::x_OnChangeData(), CFilterDlg::x_OnChangeMode(), CFilterDlg::x_OnChangeName(), CAlignMarkHandler::x_OnChangeSelRange(), CWMTabControl::x_OnCloseTab(), CWindowManager::x_OnContainerUpdateCommand(), CFilterDlg::x_OnDeleteCurrent(), CSequenceGotoDlg::x_OnGoto(), CGBenchWindowManager::x_OnInsertContainer(), CTextSelHandler::x_OnMouseMove(), CWindowManager::x_OnPseudoCommand(), CGBenchWindowManager::x_OnSaveLayout(), CSeqMarkerSetDlg::x_OnSet(), CGFFReader::x_ParseV2Attributes(), CSeqVector_CI::x_PrevCacheSeg(), CWindowManager::x_PutClientInFrame(), CWindowManager::x_PutClientInTab(), CTar::x_ReadAndProcess(), CStudyPreviewData::x_ReadData(), CStudyLoader::x_ReadData(), CRuler::x_RenderAllPosLabels(), CHistogramGraph::x_RenderBarChart(), CTraceGraph::x_RenderConfGraph(), CHistogramGraph::x_RenderIntensity(), CBlastOptionsRemote::x_ResetValue(), CFeaturesPanelIR::x_SelObjectInRect(), CMasterContext::x_SetBaseName(), CCommentItem::x_SetCommentWithURLlinks(), CMenu::x_SetItems(), CBioseq_CI::x_SkipClass(), x_SpaceToDash(), CDiagPanel::x_StyleParse(), CViewAsn::x_StyleParse(), IPhyloTreeRenderer::x_TestForNode(), CGlBitmapFont::x_Truncate(), CSnpFilterListDialog::x_UpdateBrowser(), CWindowManager::x_UpdateDockCommand(), CFilterDlg::x_UpdateSelected(), CWindowManager::x_WrapClientInTabControl(), CElementaryMatching::x_WriteIndexFile(), and CBDB_CacheIReader::~CBDB_CacheIReader().

CRange<TSeqPos> range1

Definition at line 177 of file seq_map_switch.cpp. Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc::Compare(), CAnnotCompare::CompareFeats(), SRangeStartSort::operator()(), CReadBlastApp::printOverlapReport(), CAutoDefExonListClause::SeqLocIntersect(), CMultiAligner::x_ComputeProfileRangeAlignment(), CCrossPanelIR::x_DrawCrossAlignment(), and x_RemoveEnvelopedSubHits().

CRange<TSeqPos> range2

Definition at line 179 of file seq_map_switch.cpp. Referenced by CSubjectRanges::AddRange(), BOOST_AUTO_TEST_CASE(), CSeq_loc::Compare(), CAnnotCompare::CompareFeats(), SRangeStartSort::operator()(), CReadBlastApp::printOverlapReport(), CAutoDefExonListClause::SeqLocIntersect(), CMultiAligner::x_ComputeProfileRangeAlignment(), CCrossPanelIR::x_DrawCrossAlignment(), and x_RemoveEnvelopedSubHits().

bool same_strand

Definition at line 180 of file seq_map_switch.cpp. Referenced by CCompareSeq_locs::x_ComputeOverlapValues().

bool skip

Definition at line 204 of file seq_map_switch.cpp. Referenced by DTDParser::ConsumeElementContent(), AbstractLexer::FillChar(), CChainer::CChainerImpl::FilterOutInferiorProtAlignmentsWithIncompatibleFShifts(), CAlignmentRefiner::GetBlocksToAlign(), CSeqMap_CI_SegmentInfo::GetRefPosition(), CStringUTF8::GuessEncoding(), CProjBulderApp::Gui_ConfirmConfiguration(), norm_fmt(), CTitleProcess::ProcessInitialize(), CAsn2Asn::RunAsn2Asn(), s_BlastCompressedAaScanSubject(), s_CompressedLookupAddUnencoded(), s_FindUnusedLines(), s_GetInfo(), s_GetNextInfo(), s_Open(), s_ReportUnusedLine(), s_TokenizeString(), COffsetList::Save(), SERV_GetInfoEx(), SERV_GetInfoP(), SERV_OpenEx(), SERV_OpenP(), Server_CheckLineMessage(), CSeqVector_CI::SkipGap(), CSeqVector_CI::SkipGapBackward(), CObjectIStream::UpdateSkipUnknownMembers(), CObjectIStream::UpdateSkipUnknownVariants(), CWig2tableApplication::x_GetParamName(), CWig2tableApplication::x_GetPos(), CSeqMap_CI_SegmentInfo::x_GetSkipAfter(), CSeqMap_CI_SegmentInfo::x_GetSkipBefore(), CObjectIStream::x_GetSkipUnknownDefault(), CWig2tableApplication::x_GetWord(), CAlnMap::x_SkipType(), CWig2tableApplication::x_SkipWS(), CWig2tableApplication::x_TryGetDoubleSimple(), and CDockSplitter::x_UpdateClientsState().

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