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NCBI C++ ToolKit: Seq-loc Management

inline \

void CSeq_loc::Set##x(

##x& v) \

{ \

InvalidateCache(); \

Tparent::Set##x(v); \

} \

{ \

InvalidateCache(); \

return Tparent::Set##x(); \

}

Definition at line 966 of file Seq_loc.hpp.

Definition at line 392 of file Seq_loc.hpp.

Flags for location comparison.

Definition at line 244 of file Seq_loc.hpp.

Options for empty locations processing.

ignore empty locations

treat empty locations as usual

Definition at line 456 of file Seq_loc.hpp.

This enum defines a way equiv sets are expanded or created when one of Insert*() methods is called.

By default no equiv sets are created or expanded except if insertion point is completely inside of an equiv or its part.

A new equiv set will be created, even if the insertion point is already inside of an existing equiv, so that new equiv set may become a sub-unit of an exisiting equiv set.

The new equiv set will contain one part with the inserted element as its content. The mode will switch to eEquiv_append after the insertion.

New equiv part will be started with the inserted element.

If the insertion point is not in or near any existing equiv part then exception is thrown. If... A. the insertion point is exactly between two equiv sets then a new equiv part will be created at the end of the first set with the inserted element as its content. B. the insertion point is at a boundary of any equiv part then a new equiv part will be created at this point with the inserted element as its content. C. the insertion point is in the middle of existing part then the existing part will be split at the insertion point and new element will be added to the second part after splitting.

The mode will switch to eEquiv_append after the insertion.

If the insertion point is just after any equiv part, including the last one in an equiv, then the inserted element is appended to the part, and the equiv mode will remain eEquiv_append.

Otherwise the equiv mode will switch to eEquiv_none. Change the mode to eEquiv_none explicitly if you want to stop expanding existing equiv.

If the insertion point is just before any equiv part, including the first one in an equiv, then the inserted element is prepended to the part, and the equiv mode will remain eEquiv_prepend.

Otherwise the equiv mode will switch to eEquiv_none. Change the mode to eEquiv_none explicitly if you want to stop expanding existing equiv.

Definition at line 760 of file Seq_loc.hpp.

Seq-loc is not set.

Seq-loc on multiple ids when one id is required.

Seq-loc has data that is not supported yet.

Seq-loc is incorrectly formed.

Seq-loc iterator is in bad state.

Seq-loc type is incompatible with operation.

parameter is out of valid range

Definition at line 76 of file Seq_loc.hpp.

Options for creation modified locations Bond and equiv types are preserved if possible.

use most compact Seq-loc type (default)

keep original Seq-loc type if possible

Definition at line 597 of file Seq_loc.hpp.

CSeq_loc operations.

Flags for operations: fStrand_Ignore - if set, strands will be ignored and any ranges may be merged/sorted. If not set, ranges on plus and minus strands are treated as different sub-sets. In some operations strand may still be checked (see fMerge_Abutting and order of ranges).

NOTE: merge flags do not sort ranges, so only overlaps bewtween neighbor ranges can be detected. To merge all overlappig ranges add fSort flag. The only exception is fSortAndMerge_All which already includes fSort;

fMerge_Contained - merges (removes) any range which is completely contained in another range. fMerge_Abutting - merge abutting ranges. Also forces merging of contained ranges. Even if fStrand_Ignore is set, only the ranges with the correct order are merged (e.g. loc2.to == loc1.from must be true if loc1.strand is minus). fMerge_Overlapping - merge overlapping ranges. Also forces merging of contained ranges. fMerge_All - merge any ranges if possible (contained, overlapping, abutting). The flag does not force sorting, so only neighbor ranges can be merged. To sort ranges before merging add fSort flag or use fSortAndMerge_All. fSortAndMerge_All - combination of fSort and fMerge_All. fMerge_SingleRange - creates a single range, covering all original ranges. Strand is set to the first strand in the original seq-loc, regardless of the strand flag.

fSort - forces sorting of the resulting ranges. All ranges on the same ID are grouped together, but the order of IDs is undefined. Strand is preserved if all values having the same direction are equal. Otherwise strand is reset to plus and minuns (in strand-preserve mode) or unknown (in strand-ignore mode). NULLs are always merged to a single NULL. The order of locations for each ID is: NULL, whole, empty, plus strand intervals, minus strand intervals.

Definition at line 324 of file Seq_loc.hpp.

Iterate sub-locations in positional order.

Iterate sub-locations in biological order

Definition at line 460 of file Seq_loc.hpp.

Simple adding of seq-locs.

Definition at line 3875 of file Seq_loc.cpp.

References CSeq_loc_equiv::Add(), CPacked_seqint::AddInterval(), CPacked_seqint::AddIntervals(), CPacked_seqpnt::AddPoint(), CPacked_seqpnt::AddPoints(), CSeq_loc_mix::AddSeqLoc(), CSeq_loc::Assign(), 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::GetInt(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CPacked_seqpnt_Base::GetPoints(), CSeq_loc::InvalidateCache(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), NCBI_THROW_FMT, s_CanAdd(), CSeq_loc_Base::SelectionName(), CSeq_loc::SetEquiv(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc_Base::Which(), CSeq_loc::x_ChangeToMix(), CSeq_loc::x_ChangeToPackedInt(), and CSeq_loc::x_ChangeToPackedPnt().

Referenced by FeatUtil::AddLocations(), CAutoDefFeatureClause::CAutoDefFeatureClause(), ExtendCDSToStopCodon(), ExtendToStopCodon(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CValidError_bioseq::GetLocFromSeq(), GetSeqExt(), C5ColImportData::Initialize(), CLocMapper_Default::Map(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CCompareSeqRegions::NextComparisonGroup(), s_CombineDustMasksWithUserProvidedMasks(), variation_ref::CVariationUtil::s_FactorOutLocsInPlace(), s_GetMaskLoc(), s_GetUngapLoc(), s_MakeNewMasterSeq(), CGetSeqLocFromStringHelper::Seq_loc_Add(), Seq_loc_Add(), Seq_locs_Merge(), CGeneFinder::CGeneSearchPlugin::setUpFeatureIterator(), SplitLocationForGap(), TruncateSeqLoc(), CMaskedRangeSet::x_CombineLocs(), CSGAlignmentJob::x_CreateFeatGlyph(), CWindowMaskerJob::x_CreateProjectItems(), CFeaturePropagator::x_ExtendToStopCodon(), variation::CVariationUtil::CCdregionIndex::x_Index(), CXcompareAnnotsApplication::x_ProcessMappingRange(), CNewCleanup_imp::x_SeqFeatRnaGBQualBC(), CSeq_loc_Mapper_Base::x_StripExtraneousFuzz(), x_ToBlastVec(), CFeaturePropagator::x_TruncateToStopCodon(), CGtfWriter::xWriteFeatureExons(), and CBedWriter::xWriteFeaturesTracked().

Override Assign() to incorporate cache invalidation.

Reimplemented from CSerialObject.

Definition at line 337 of file Seq_loc.cpp.

References CSeq_id::Assign(), CSerialObject::Assign(), 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::GetBond(), CSeq_loc_Base::GetEmpty(), CSeq_loc_Base::GetEquiv(), CSeq_loc_Base::GetFeat(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSerialObject::GetThisTypeInfo(), CSeq_loc_Base::GetWhole(), CSeq_loc::InvalidateCache(), CSeq_loc_Base::Reset(), CSeq_loc::SetBond(), CSeq_loc::SetEmpty(), CSeq_loc::SetEquiv(), CSeq_loc::SetFeat(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetNull(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CSeq_loc::SetWhole(), CSeq_loc_Base::Which(), and x_Assign().

Referenced by CSeq_loc_equiv::Add(), CSeq_loc::Add(), FeatUtil::AddLocations(), CSeq_loc_mix::AddSeqLoc(), CEditSequence::AdjustFeatureLocations(), CCDSTranslationPanel::AdjustForStopCodonHyperlinkClicked(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), AdjustMappedStop(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), CFeatGapInfo::AdjustProteinSeq(), CFeatTrim::Apply(), CFuseJoinsInLocs::apply(), CAdjustFeatsForIntrons::apply(), CCreateLocusTagGene::apply(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CBedImportData::CBedImportData(), CCompareSeq_locs::CCompareSeq_locs(), CGtfImportData::CGtfImportData(), CSeq_loc::ChangeToMix(), CWriteUtil::ChangeToPackedInt(), CSeq_loc::ChangeToPackedInt(), CMultiSeqInfo::CMultiSeqInfo(), CollapseDiscontinuitiesInUTR(), CFixForTransSplicing::CombineFeatures(), variation::Contains(), CConvertCDSToMiscFeat::Convert(), CLocationEditPolicy::ConvertToJoin(), CLocationEditPolicy::ConvertToOrder(), CQueryFactoryInfo::CQueryFactoryInfo(), CAlignmentAssistant::CreateFeature(), CEditSequence::CreateFeature(), variation_ref::CVariationUtil::CreateFlankLocs(), variation::CVariationUtil::CreateFlankLocs(), CEditSequence::CreateRegulatory(), CStd_seg::CreateRowSeq_loc(), ExtendCDSToStopCodon(), ExtendStop(), ExtendToStopCodon(), CProSplign::FindGlobalAlignment(), CProSplign::CImplementation::FindGlobalAlignment_stage1(), FindNewLocations(), IEditingActionFeat::FindOrCreateProtFeat(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), variation::FindSSRLoc(), CFlatAnticodonQVal::Format(), fta_seqloc_del_far(), fta_seqloc_local(), CGeneFinder::GeneSearchNormalizeLoc(), variation::CVariationUtil::CCdregionIndex::Get(), CFindRSites::GetAnnot(), CMacroBioData_FeatIterBase::GetBestDescr(), CMacroBioData_FeatIntervalIter::GetBestDescr(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), CCdsFromGeneMrnaExon::GetCommand(), CFuseFeaturesDlg::GetCommand(), CGeneFeatFromOtherFeatDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), CGeneFeatFromXrefs::GetCommand(), CValidErrorFormat::GetFeatureLocationLabel(), CValidErrorFormat::GetFeatureProductLocLabel(), CGeneFinder::GetFeatViaSubsetThenExtremesIfPossible(), CProteinAlignText::GetGenomicBounds(), variation::CVariationUtil::CVariantPropertiesIndex::GetLocationProperties(), GetOverlappingFeatures(), GetProductLabel(), GetSeqLocation(), GetSeqLocDescription(), CAlignGlyph::GetSignature(), GetSourceFeatForProduct(), CFeatGlyph::GetTooltip(), CWriteUtil::GetTranssplicedEndpoints(), GetValidatorLocationLabel(), CNSeq::Init(), CGffFeatureRecord::InitLocation(), MakemRNAforCDS(), CAliToSeq_align::MakeSeq_align(), CIdMapper::Map(), CLocMapper_Default::Map(), CGencollIdMapper::Map(), CCdsToMatPeptide::MergeConvert(), NormalizeLoc(), variation::SFastLocSubtract::operator()(), PatchTargetSequence(), CBedAnnotAssembler::ProcessRecord(), variation::CVariationUtil::RemapToAnnotatedTarget(), s_FlattenLoc(), s_GetClipLoc(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetIntronsAndSpliceSiteLocs(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetUTRLocs(), s_HasMobileElementForInterval(), s_LocationJoinToOrder(), s_NormalizeNullsBetween(), CSequenceUpdater::s_OffsetLocation(), s_UpdateCodeBreaksAndAnticodons(), CClippedScorer::ScoreAlignments(), CNewCleanup_imp::SeqLocBC(), CCleanup::SeqLocExtend(), CSeq_loc_Mapper_Message::SetLoc(), CCDSTranslationPanel::SetProduct(), variation_ref::CVariationUtil::SetVariantProperties(), CFeatGapInfo::Split(), SrchGene(), CAlignmentAssistant::TranslateLocations(), CFeatGapInfo::Trim(), TruncateSeqLoc(), UpdateToBestId(), CUCSCRegionWriter::WriteAnnot(), CFeatGapInfo::x_AdjustCodebreaks(), variation::CVariationUtil::x_AdjustDelinsToInterval(), CFeatGlyph::x_AdjustFrame(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), variation_ref::CHgvsParser::x_AsHgvsExpression(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CFastaExportJob::x_CheckForDuplicates(), CFlatGatherer::x_CollectSourceFeatures(), CCompareSeq_locs::x_Compare(), variation_ref::CHgvsParser::x_conversion(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CFeatureGenerator::SImplementation::x_CreateNcRnaFeature(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CGBankLoadingJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CFeaturePropagator::x_ExtendToStopCodon(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), x_GetBestOverlapForSNP(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CAsn2FlatApp::x_GetLocation(), CEditingBtnsPanel::x_GetSelectedLocations(), x_GetSourceFeatViaCDS(), IEditingActionFeat::x_GetSublocOnBioseq(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CEditObjectSeq_feat::x_HandleCdsProduct(), variation_ref::CHgvsParser::x_identity(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), variation_ref::CHgvsParser::x_InstToString(), CGencollIdMapper::x_Map_OneToOne(), CGencollIdMapper::x_Map_Up(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CSequenceUpdater::x_MappedFeature_ChangeId(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation_ref::CHgvsParser::x_nuc_inv(), variation::CHgvsParser::x_seq_loc(), CBioseqContext::x_SetLocation(), CCDSTranslationPanel::x_SetLocationForProtein(), variation_ref::CHgvsParser::x_ssr(), CSeq_loc_Mapper_Base::x_StripExtraneousFuzz(), CFeatTrim::x_TrimCodeBreak(), CFeatTrim::x_TrimTrnaExt(), CFeaturePropagator::x_TruncateToStopCodon(), CModifySeqId::x_UpdateLoc(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), CGff3Writer::xAssignFeature(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), and CExonNumberAssigner::xInitialize().

Definition at line 3633 of file Seq_loc.cpp.

References CSeq_loc_mix::AddSeqLoc(), CSeq_loc::Assign(), CSeq_loc::CSeq_loc(), CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Packed_int, eShallow, NON_CONST_ITERATE, CSeq_loc_mix_Base::Set(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), and CSeq_loc_Base::Which().

Referenced by variation::FindSSRLoc(), CLocMapper_Default::Map(), s_CalcCoverageCount(), CSeq_loc::x_ChangeToMix(), CCompareSeq_locs::x_Compare(), CCompareSeq_locs::x_ComputeOverlapValues(), CFeaturePropagator::x_MapLocation(), x_PushRange(), CFeatTableEdit::xGetGeneLocation(), and CGff3LocationMerger::xGetRecordLocation().

Works only if location is currently an interval, point, packed-int (handled trivially), or a mix built recursively from these.

Definition at line 3670 of file Seq_loc.cpp.

References CPacked_seqint::AddInterval(), CSeq_loc::Assign(), CSeq_loc::ChangeToPackedInt(), copy(), 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_Pnt, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, Get(), CSeq_point_Base::GetFuzz(), CSeq_loc::GetId(), CSeq_loc_Base::GetInt(), CInt_fuzz_Base::GetLim(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPnt(), CSeq_loc::GetStrand(), CInt_fuzz_Base::IsLim(), CSeq_loc::IsSetStrand(), ITERATE, NCBI_THROW_FMT, CSeq_loc_Base::SelectionName(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_interval_Base::SetId(), CSeq_loc::SetPacked_int(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), ncbi::grid::netcache::search::fields::size, and CSeq_loc_Base::Which().

Referenced by CWriteUtil::ChangeToPackedInt(), CSeq_loc::ChangeToPackedInt(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CWriteUtil::GetTranssplicedEndpoints(), CGtfLocationMerger::MergeLocationForGene(), s_CombineDustMasksWithUserProvidedMasks(), s_GetMaskLoc(), s_GetUngapLoc(), TruncateToCDS(), CUCSCRegionWriter::WriteAnnot(), CSeq_loc::x_ChangeToPackedInt(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_MapFeature(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), CExonNumberAssigner::xInitialize(), and CGtfWriter::xWriteFeatureExons().

Compare locations by total range for each seq-id.

Compares seq-ids (

See also

CSeq_loc::CompareOrdered()), then compares total range starts (left to right) and lengths (longerst first). Optionally compares strands; location without strand goes first.

Definition at line 596 of file Seq_loc.cpp.

References CSeq_loc::CSeq_loc(), CSeq_id_Base::e_not_set, CSeq_loc_CI::eEmpty_Allow, CSerialObject::Equals(), flags, CSeq_loc::GetId(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_Base::IsMix(), NULL, CSeq_loc::SetMix(), tmp, CSeq_id_Base::Which(), and CSeq_loc::x_CompareSingleId().

Compare first-level sub-locations sequentially to order them by biological "complexity".

More "complex" location will come last. Sub-locations are checked in Seq-loc-mix and Packed-seqint. Minus strand locations' order is reversed. Seq-ids are not checked in this method, unless you set filter, which will allow the user to pick which parts to skip.

Definition at line 805 of file Seq_loc.cpp.

References Get(), CPacked_seqint_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), IsReverse(), and s_CompareIntervals().

Referenced by CSeq_feat::CompareNonLocation(), CSeqUtils::GetCdsMappingInfoFromRna(), and CAnnotObjectType_Less::operator()().

Definition at line 82 of file Seq_loc.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::InvalidateCache(), CSeq_loc::SetBond(), CSeq_loc::SetEmpty(), CSeq_loc::SetEquiv(), CSeq_loc::SetFeat(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetNull(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc::SetWhole().

Delete current element, and make iterator to point to the next element.

All other iterators of the same CSeq_loc object will become invalid. If the deleted element is contained in any equiv set then the equiv set and its corresponding part will be reduced in size appropriately, and if the part and/or the set become empty after the deletion they will be removed completely.

Definition at line 2724 of file Seq_loc.cpp.

References CSeq_loc_CI_Impl::DeleteRange(), CSeq_loc_CI::m_Impl, CSeq_loc_CI::m_Index, and CSeq_loc_CI::x_CheckValid().

Referenced by CEditSequence::AdjustFeatureLocations(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), CEditSequence::AdjustProtFeatureLocations(), CFuseJoinsInLocs::apply(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CAlignmentAssistant::TranslateLocations(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), IEditingActionFeat::x_GetSublocOnBioseq(), and CFeaturePropagator::x_MapLocation().

Flip the strand (e.g. plus to minus)

Definition at line 3969 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CPacked_seqint::FlipStrand(), CPacked_seqpnt::FlipStrand(), CSeq_interval::FlipStrand(), CSeq_loc_mix::FlipStrand(), CSeq_point::FlipStrand(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().

Referenced by CRevIntPanel::AddCommand(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), x_GetBestOverlapForSNP(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), variation_ref::CHgvsParser::x_InstToString(), and variation_ref::CHgvsParser::x_seq_loc().

Get the nearest seq-loc containing the current range.

For packed/mixed locations the embedding seq-loc may include other ranges.

Note

Don't ever confuse it with GetRangeAsSeq_loc!

Definition at line 2573 of file Seq_loc.cpp.

References eNotSet, SSeq_loc_CI_RangeInfo::m_Loc, NCBI_THROW, CSeq_loc_CI::x_CheckValid(), and CSeq_loc_CI::x_GetRangeInfo().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), CFeatureGenePanel::GetLocationForGene(), CSeq_loc_CI::GetSeq_loc(), s_GetCdregionPlusUpstream(), s_LocationJoinToOrder(), s_LocationToStartStopPairs(), s_SeqLocAnyNull(), SeqLocPartialCheck(), and CFlatSeqLoc::x_Add().

Get the id of the location return NULL if has multiple ids or no id at all.

Definition at line 941 of file Seq_loc.hpp.

References CSeq_loc::CheckId(), and NULL.

Referenced by AddCodeBreak(), AddColumnsToFeatureTable(), CIdMapper::AddMapping(), CCleanup::AddProtein(), AddProteinFeature(), CImportFeatTable::AddSeqAnnotToSeqEntry(), CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CEditSequence::AdjustFeatureLocations(), AdjustMappedStop(), variation::AdjustMoltype(), CFeatGapInfo::AdjustProteinSeq(), AdjustSingleFeature(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), ApplyFeatureSeqTableToSeqEntry(), variation::CVariationUtil::AsVariation(), variation::CHgvsParser::AttachHgvs(), variation::CVariationUtil::AttachProteinConsequences(), CDiscrepancyVisitorImpl< _Name >::Autofix(), Blast_FindWindowMaskerLoc(), BOOST_AUTO_TEST_CASE(), BuildFeatureSeqTableFromSeqEntry(), CNewCleanup_imp::CdregionFeatBC(), CSeq_loc::ChangeToPackedInt(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CheckForeignLoc(), variation::CVariationUtil::CheckPlacement(), CIdRangeMap::CIdRangeMap(), IProjectViewFactory::CombineObjects(), CTableViewWithTextViewNav::CombineObjects(), CSeq_loc::Compare(), CFeaturePropagator::ConstructProteinFeatureForPropagatedCodingRegion(), COrfSearchForm::ConstructQuery(), CSequenceSearchForm::ConstructQuery(), CVariationNormalizationDelIns::ConvertExpandedInsertionToDelIns(), CProteinAlignText::CProteinAlignText(), CCreateProteinId::create_protein_ids(), CAlignmentAssistant::CreateFeature(), CEditSequence::CreateFeature(), variation::CVariationUtil::CreateFlankLocs(), CGuiObjectInfoComponent::CreateObject(), CGuiObjectInfoSeq_feat::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), CGuiSeqInfoSeq_id::CreateObject(), CEditSequence::CreateRegulatory(), CRemoveName::CRemoveName(), CSeqVector::CSeqVector(), DoImportFTable(), CGBObjectLoader::Execute(), ExtendCDSToStopCodon(), ExtendLocationForTranslExcept(), ExtendStop(), CCleanup::ExtendStopPosition(), ExtendToStopCodon(), CAnnotationASN1::ExtractModels(), FinalCleanup(), CProSplign::FindGlobalAlignment(), variation::CVariationUtil::FindLocationProperties(), CInternalStopFinder::FindStartStopRanges(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), FormatAsAsn(), fta_seqloc_del_far(), FTASeqLocCheck(), NSearchFeatPanel::GatherFeatures(), GetAccessionFromObjects(), CGenbankIdResolve::GetBestId(), CSeqUtils::GetCdsMappingInfoFromRna(), GetCdsOnMrna(), GetCDSProductSeq(), CExonFromCds::GetCommand(), CExtendCDSToStop::GetCommand(), CSNPTableModel::GetExtraValueAt(), CSeqUtils::GetFeatLocation(), CAddFeatureBetweenDlg::GetFeatureLocations(), CFeatGlyph::GetHTMLActiveAreas(), CBioseqSeqInfoSrc::GetId(), CSeq_featHandler::GetLabel(), GetLastCodonLoc(), CVecscreenRun::GetList(), CAnnotMapping_Info::GetLocationId(), CSeq_feat_Handle::GetLocationId(), CSeqUtils::GetMappingInfo(), GetOverlappingFeatures(), CAnnotMapping_Info::GetProductId(), CSeq_feat_Handle::GetProductId(), CCleanup::GetProteinLocationFromNucleotideLocation(), CCleanup::GetProteinName(), GetProteinString(), CCodingPropensity::GetScore(), CSeq_align::GetSeq_id(), IRepeatRegion::GetSeqIdString(), CWriteUtil::GetStringId(), CBlastQuerySourceOM::GetTitle(), CFeatGlyph::GetTooltip(), CGuiObjectInfoClone::GetToolTip(), CSeqIdField::GetVal(), CEditingActionFeatTranslation::GetValue(), CEditingActionFeatTranscriptId::GetValue(), CAsn2FastaApp::HandleSeqEntry(), CNewCleanup_imp::ImpFeatBC(), InheritPartialness(), CNSeq::Init(), CSeqTextPanel::InitObject(), IsGeneLocationOk(), IsOneBioseq(), CEditingActionFeatTranslation::IsSetValue(), CEditingActionFeatTranscriptId::IsSetValue(), MakeGeneForFeature(), MakemRNAforCDS(), MakeTrnaWithAnticodon(), CIdMapper::Map(), CCdsToMatPeptide::MergeConvert(), CGtfLocationMerger::MergeLocationForGene(), CFeatureGenerator::SImplementation::MergeSeq_locs(), variation::SFastLocSubtract::operator()(), operator<<(), PackSeqPntCheckCpp(), CCleanup::ParseCodeBreak(), PatchTargetSequence(), CTabularFormatter_SeqId::Print(), ProjectExons(), CGFFReader::Read(), CHgvsReader::ReadSeqAnnot(), CFeature_table_reader::ReadSequinFeatureTables(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), RemapAlignToLoc(), variation::CVariationUtil::RemapToAnnotatedTarget(), CCdsToMatPeptide::RemoveProteins(), RenameGeneratedBioseqs(), RestoreModelFromPublicMrnaFeature(), RestoreModelReadingFrame(), RetrievePartsOfLargeChromosome(), CNewCleanup_imp::RnaFeatBC(), CFeatureRetrievalJob::Run(), CVectorScreen::Run(), CDemoApp::Run(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_AddTopLevelGenomicLinks(), s_BLAST_OneSubjectResults2CSeqAlign(), s_CheckIfMatchesBioseq(), s_ChrName(), s_CombineRefs(), s_CreateMappingInfo(), s_DumpSequences_wRange(), s_EliminateDuplicates(), variation::CVariationUtil::s_FindConsequenceForPlacement(), s_GetAnnotId(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), s_GetmRNAForCDS(), s_GetProductIdOrLocusTag(), s_GetRnaMappingLocs(), s_IdXrefsNotReciprocal(), s_IsVirtualLocation(), s_LocSortCompare(), s_ParseTRnaFromAnticodonString(), s_PartialAtGapOrNs(), s_TestForOverlapEx(), SeqIntCheckCpp(), SeqLocExtend(), CCleanup::SeqLocExtend(), CAutoDefExonListClause::SeqLocIntersect(), CFeatureSearchJob::SeqLocToString(), SeqPntCheckCpp(), CReportEntry::SetCds(), CReportEntry::SetMrna(), CEditingActionFeatTranslExcept::SetValue(), CFeatGapInfo::Split(), StartAbutsGap(), StopAbutsGap(), TransferPartialness(), Translate(), TranslateCDSCommand(), CFeatGapInfo::Trim(), TruncateSeqLoc(), CMolTypeValidator::Validate(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateSeqFeatContext(), CCleanup::WGSCleanup(), CUCSCRegionWriter::WriteAnnot(), CFastaOstreamEx::WriteFeature(), CFastaOstreamEx::x_AddProteinIdAttribute(), CFastaOstreamEx::x_AddProteinNameAttribute(), CFeatureItem::x_AddQualProteinConflict(), CFeatureItem::x_AddQualsCdregionIdx(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsRna(), CFastaOstreamEx::x_AddTranscriptIdAttribute(), CEditObjectSeq_feat::x_AdjustCircularGene(), CEditObjectSeq_feat::x_AdjustGene(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), variation::CHgvsParser::x_AsHgvsExpression(), variation::CHgvsParser::x_AsHgvsInstExpression(), CSGFeatureJob::x_CalcIntervals(), CFastaExportJob::x_CheckForDuplicates(), CFeatureGenerator::SImplementation::x_CheckInconsistentDbxrefs(), CSeqdesc_CI::x_CheckRef(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CCorrectGenesDialog::x_CorrectPairInterval(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CImportFeatTable::x_CreateCommand(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CSGFeatureJob::x_CreateFeature1(), CGFFReader::x_CreateGeneFeatures(), CBLASTSeqToolJob::x_CreateProjectItems(), CTaxTreeToolJob::x_CreateProjectItems(), CProSplignJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CImportFeatTable::x_DoImportCDS(), CAdjustFeaturesForGaps::x_DoOne(), CFeatGlyph::x_DrawProjectedRuler(), CFeatGlyph::x_DrawRuler(), CNewCleanup_imp::x_ExtendFeatureToCoverSequence(), CFeaturePropagator::x_ExtendToStopCodon(), CImportFeatTable::x_FindLocalBioseq_Handle(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CDBSourceItem::x_GatherInfo(), CFeatureItem::x_GetAssociatedProtInfo(), CFeatureItem::x_GetAssociatedProtInfoIdx(), CClonePlacementGlyph::x_GetCloneEnds(), CCreateGeneModelTask::x_GetCommand(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CGuiObjectInfoSeq_feat::x_GetFeatLocation(), CFastaOstreamEx::x_GetOtherIdString(), CGuiObjectInfoSeq_feat::x_GetProductLengthRow(), CClonePlacementGlyph::x_GetSupportTypeForNonPrototypeEnds(), CAlignedFeatureGraph::x_GetTooltip(), CFastaExportJob::x_GetWholeLoc(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CValidError_bioseq::x_IdXrefsNotReciprocal(), variation::CVariationUtil::CCdregionIndex::x_Index(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), variation::CVariationUtil::x_InferNAfromAA(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CCdregionValidator::x_IsProductMisplaced(), CSGAlignmentJob::x_LoadAlignmentFeats(), CBatchFeatJob::x_LoadFeatProducts(), CGencollIdMapper::x_Map_Up(), CFeatureGenerator::SImplementation::x_MapFeature(), CNewCleanup_imp::x_MoveCdregionXrefsToProt(), CRNAPanel::x_PopulateTranscriptID(), CFlatGatherer::x_PrepareAnnotDescStrucComment(), variation::CVariationUtil::x_Remap(), CValidError_bioseq::x_ReportOverlappingPeptidePair(), CVecscreenRun::x_RunBlast(), CProSplignJob::x_RunProSplign(), CFeatureSearchJob::x_SearchForSNP(), CSequenceSearchJob::x_SearchSequence(), CBLASTToolManager::x_SelectCompatibleInputObjects(), CProSplignTool::x_SelectCompatibleInputObjects(), CSplignTool::x_SelectCompatibleInputObjects(), CWindowMaskerTool::x_SelectCompatibleInputObjects(), CNewCleanup_imp::x_SeqFeatCDSGBQualBC(), CFeatureGenerator::SImplementation::x_SetComment(), CFeatureGenerator::SImplementation::x_SetExceptText(), CCDSTranslationPanel::x_SetLocationForProtein(), CReportEntry::x_SetRnaCds(), CVariationNormalization_base< T >::x_Shift(), CAlignTabExportPage2::x_StartAlignNamesJob(), CAlignTabExportPage2::x_StartNAAlignNamesJob(), CValidError_bioseq::x_TranscriptIDsMatch(), CFastaOstreamEx::x_TrimLocation(), CFeaturePropagator::x_TruncateToStopCodon(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CModifySeqId::x_UpdateLoc(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CSingleFeatValidator::x_ValidateExceptText(), CCdregionValidator::x_ValidateFarProducts(), CValidError_graph::x_ValidateGraphLocation(), CSingleFeatValidator::x_ValidateSeqFeatLoc(), CValidError_align::x_ValidateSeqLength(), CGff3Writer::xAssignFeature(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff2Writer::xAssignFeatureAttributeProteinId(), CFeatTableEdit::xConvertToGeneralIds(), CFeatTableEdit::xGetGeneLocation(), CGff3ImportData::xInitializeDataCds(), XISAGappedSeqLoc(), CFeatureTableReader::xMoveCdRegions(), CWiggleWriter::xTableGetChromName(), CBedGraphWriter::xWriteAnnotSeqTable(), CGff3Writer::xWriteFeatureCds(), and CWiggleWriter::xWriteSingleGraphFixedStep().

Appends a label suitable for display (e.g., error messages) label must point to an existing string object Method just returns if label is null.

Note this label is NOT GenBank-style.

Definition at line 3467 of file Seq_loc.cpp.

References label, and s_GetLabel().

Referenced by COrfSearchForm::ConstructQuery(), CExploreProcess::DoOneBioseq(), fta_fix_seq_loc_id(), CMacroBioData_FeatIterBase::GetBestDescr(), CMacroBioData_FeatIntervalIter::GetBestDescr(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), CWriteUtil::GetCodeBreak(), CBulkGene::GetCommandFromValuesTable(), CBulkMiscFeat::GetCommandFromValuesTable(), CBulkRna::GetCommandFromValuesTable(), CDesktopGraphItem::GetDescription(), GetIdStartStopStrandStr(), GetLocationStr(), CSequenceUpdater::GetNotImportedFeatsReport(), GetProductLabel(), GetSeqLocDescription(), GetValidatorLocationLabel(), CBulkGene::GetValuesTableFromSeqEntry(), CBulkMiscFeat::GetValuesTableFromSeqEntry(), CBulkRna::GetValuesTableFromSeqEntry(), location_to_string(), CLocMapper_Default::Map(), CIdMapper::MapErrorString(), CCompareSeqRegions::NextComparisonGroup(), SFeats_OpLess::operator()(), COverlapPairLess::operator()(), CValidError_imp::PostErr(), PrintPntAndPntsUseBestID(), CFeaturePropagator::Propagate(), objects::CFixSuspectProductName::ReportFixedProduct(), SRelLoc::Resolve(), s_GetFeatDesc(), s_GetGeneTextLabel(), s_GetLabel(), CCompareFeats::s_GetLocLabel(), s_GetMrnaProductString(), SeqLocHaveFuzz(), SeqLocPrintUseBestID(), SeqLocString(), CGeneOverlapProcess::SeqLocString(), CGeneFeatTreeProcess::SeqLocString(), CSeqUtils::SeqLocToBioseq(), CFeatureSearchJob::SeqLocToString(), CValidError_bioseq::ValidateDeltaLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CCompareSeqRegions::x_GetPutativeMatches(), CXcompareAnnotsApplication::x_ProcessComparison(), CXcompareAnnotsApplication::x_ProcessMappingRanges(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CFeaturePropagator::x_PropagatetRNA(), CSequenceUpdater::x_ShouldImportFeature(), and CValidError_bioseq::x_ValidateCDSVDJCmatch().

Get the range.

Definition at line 1042 of file Seq_loc.hpp.

References SSeq_loc_CI_RangeInfo::m_Range, CSeq_loc_CI::x_CheckValid(), and CSeq_loc_CI::x_GetRangeInfo().

Referenced by CEditSequence::AdjustFeatureLocations(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), CEditSequence::AdjustProtFeatureLocations(), CFuseJoinsInLocs::apply(), BOOST_AUTO_TEST_CASE(), CAnnotCompare::CompareFeats(), ConvertSeqLocsToPairwiseAln(), CLocationEditPolicy::Extend5(), CFeatureGenePanel::GetLocationForGene(), CSeqUtils::GetMappingInfoFromLocation(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), IsExtendable(), CDense_seg::RemapToLoc(), s_AdjustToAnnotatedCDS(), s_CheckAbutting(), s_CheckMixLoc(), s_CreateMappingInfo(), s_IntervalsMatchGaps(), s_IsLocationEndAtOtherLocationInternalEndpoint(), CSequenceUpdater::s_OffsetLocation(), s_PartialAtGapOrNs(), s_PrintLocAsJavascriptArray(), s_SeqLocToRangeInfoMap(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangeInfoMap(), s_SeqLocToTotalRangesInfoMapByStrand(), s_Test_CheckIntervals(), s_TestForOverlapEx(), SeqLocToBioseq(), CReportEntry::SetCds(), CAlignmentAssistant::TranslateLocations(), CGuiObjectInfoSeq_feat::x_AddExtraInfo(), CFeatGlyph::x_AdjustFrame(), CSGFeatureJob::x_CalcIntervals(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CSGAlignmentJob::x_CreateFeatGlyph(), CFeatGlyph::x_DrawRuler(), CClonePlacementGlyph::x_GetCloneEnds(), CAnnotObject_Less::x_GetExtremes(), CSeq_loc_Mapper_Base::x_GetRangeLength(), CCleanup::x_HasShortIntron(), CSeq_loc_Mapper::x_InitGCSequence(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CFeaturePropagator::x_MapLocation(), CAnnotObject_Info::x_ProcessAlign(), and CAdjustForConsensusSpliceSite::x_UpdateExonFeatures().

Get seq-loc for the current iterator position.

New CSeq_loc object may be created if the current range is a part of a packed/mixed seq-loc. The resulting seq-loc will always include only one range (which may be whole or empty).

See also

GetEmbeddingSeq_loc

Definition at line 2585 of file Seq_loc.cpp.

References ConstRef(), CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, info, CSeq_loc_CI::m_Impl, CSeq_loc_CI_Impl::MakeRangeLoc(), CRef< C, Locker >::Release(), CSeq_loc_CI::x_CheckValid(), and CSeq_loc_CI::x_GetRangeInfo().

Referenced by CAdjustForConsensusSpliceSite::AdjustCDS(), BOOST_AUTO_TEST_CASE(), CSeq_loc::Compare(), CLocationEditPolicy::ConvertToJoin(), CLocationEditPolicy::ConvertToOrder(), ExtendCDSToStopCodon(), ExtendToStopCodon(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), CExtendCDSToStop::GetCommand(), IsMixedStrandGeneLocationOk(), s_NormalizeNullsBetween(), s_PartialAtGapOrNs(), s_SeqLocEndsOnBioseq(), SeqLocExtend3(), SeqLocExtend5(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CSGFeatureJob::x_CalcIntervals(), CFeatGlyph::x_DrawFeatureBar(), CFeatGlyph::x_DrawRSites(), CFeaturePropagator::x_ExtendToStopCodon(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CSeq_loc_Mapper_Base::x_StripExtraneousFuzz(), CAdjustForConsensusSpliceSite::x_UpdateExonFeatures(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), and CAdjustForConsensusSpliceSite::x_UpdateMixLocations().

Get seq_id of the current location.

Definition at line 1028 of file Seq_loc.hpp.

References SSeq_loc_CI_RangeInfo::m_Id, CSeq_loc_CI::x_CheckValid(), and CSeq_loc_CI::x_GetRangeInfo().

Referenced by AdjustFeatureEnd3(), AdjustFeatureEnd5(), CEditSequence::AdjustFeatureLocations(), CEditSequence::AdjustProtFeatureLocations(), BadMultipleSequenceLocation(), BOOST_AUTO_TEST_CASE(), CFlatSeqLoc::CFlatSeqLoc(), CSeq_loc::Compare(), CConvertToBond::Convert(), CLocationEditPolicy::Extend3(), CLocationEditPolicy::Extend5(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), GetBioseqForSeqFeat(), GetBioseqHandleForMultihomeLocation(), CValidErrorFormat::GetFeatureBioseqLabel(), GetLocalGeneByLocus(), CFeatureGenePanel::GetLocationForGene(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), IsExtendable(), OneIdOneStrand(), s_CreateSeqAlign(), s_GetTrimmedLength(), s_SeqLocEndsOnBioseq(), s_SeqLocToRangeInfoMap(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangeInfoMap(), s_Test_CheckIntervals(), s_TestForOverlapEx(), SeqLocExtend3(), SeqLocExtend5(), UpdateToBestId(), CSGFeatureJob::x_CalcIntervals(), CSeq_loc_Mapper_Base::x_GetRangeLength(), IEditingActionFeat::x_GetSublocOnBioseq(), CSeq_loc_Mapper::x_InitGCSequence(), CSeq_loc_Mapper_Base::x_InitializeLocs(), and CAnnotObject_Info::x_ProcessAlign().

Definition at line 1035 of file Seq_loc.hpp.

References SSeq_loc_CI_RangeInfo::m_IdHandle, CSeq_loc_CI::x_CheckValid(), and CSeq_loc_CI::x_GetRangeInfo().

Referenced by BOOST_AUTO_TEST_CASE(), CFlatSeqLoc::CFlatSeqLoc(), s_CheckAbutting(), s_PrintLocAsJavascriptArray(), s_SeqLocToRangeInfoMap(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangeInfoMap(), s_SeqLocToTotalRangesInfoMapByStrand(), CAnnotObject_Less::x_GetExtremes(), and CSeq_loc_Mapper_Base::x_InitializeLocs().

Get number of ranges.

Definition at line 2636 of file Seq_loc.cpp.

References CSeq_loc_CI_Impl::GetRanges(), and CSeq_loc_CI::m_Impl.

Referenced by AdjustFeatureEnd3(), CEditSequence::AdjustFeatureLocations(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), CEditSequence::AdjustProtFeatureLocations(), CLocationEditPolicy::Extend3(), CExtendCDSToStop::GetCommand(), CLocationEditPolicy::Is3AtEndOfSeq(), IsExtendable(), s_AdjustToAnnotatedCDS(), s_CheckAbutting(), SeqLocExtend3(), CSeq_loc_CI::SetPos(), CGuiObjectInfoSeq_feat::x_AddExtraInfo(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), IEditingActionFeat::x_GetSublocOnBioseq(), and CFeaturePropagator::x_MapLocation().

Return start and stop positions of the seq-loc.

Start position is the start of the first range in the seq-loc, stop is the end of the last range. if eExtreme_Biological flag is used, the effective order of ranges and range direction depends on the strand. NOTE: The returned values are not necessarily the same as the boundaries returned by GetTotalRange(). It's also not guaranteed that the value returned by GetStart() is less or equal to the one returned by GetStop().

Definition at line 915 of file Seq_loc.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::GetBond(), COpenRange< Position >::GetFrom(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CPacked_seqint::GetStart(), CPacked_seqpnt::GetStart(), CSeq_bond::GetStart(), CSeq_interval::GetStart(), CSeq_loc_mix::GetStart(), COpenRange< TSeqPos >::GetWhole(), kInvalidSeqPos, NCBI_THROW_FMT, CSeq_loc_Base::SelectionName(), and CSeq_loc_Base::Which().

Referenced by AdjustFeatureEnd5(), CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), CEditSequence::AdjustFeatureLocations(), AdjustGene(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), CFeatGapInfo::AdjustProteinSeq(), CSplign::AlignSingleCompartment(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), ApplyPolicyToFeature(), BOOST_AUTO_TEST_CASE(), CFeatureIndex::CFeatureIndex(), Check5Extend(), CheckAdjustStart(), CheckAdjustStartAndStop(), variation_ref::CVariationUtil::CheckExonBoundary(), CIdRangeMap::CIdRangeMap(), CMatchFeat::CMatchFeat(), CFeatGapInfo::CollectGaps(), CWriteUtil::CompareFeatures(), CConvertCDSToMiscFeat::Convert(), CVariationNormalizationDelIns::ConvertExpandedInsertionToDelIns(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CEditingBtnsPanel::EditSequence(), CSequenceEditingEventHandler::EditSequence(), CCleanup::ExpandGeneToIncludeChildren(), CEditSequenceEnds::Extend5(), CExtendPartialFeatDlg::ExtendCDS(), ExtendCDSToStopCodon(), CCleanup::ExtendStopPosition(), ExtendToGapsOrEnds(), ExtendToStopCodon(), CBestFeatFinder::FindBestFeatForLoc(), FindNewLocations(), CInternalStopFinder::FindStartStopRanges(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CHTMLFormatterEx::FormatLocation(), CValidError_bioseq::GapByGapInst(), CScore_StartStopCodon::Get(), CScore_CdsScore::Get(), NSnp::GetAlleles(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), GetCdRegionCB(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeq_loc::GetCircularLength(), CExtendCDSToStop::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CAlignmentAssistant::GetFeatures(), CProteinAlignText::GetGenomicBounds(), CSeq_featHandler::GetLabel(), GetOverlappingFeatures(), CCleanup::GetProteinLocationFromNucleotideLocation(), IRepeatRegion::GetSeqPosBegin(), GetStart(), CSeq_loc_mix::GetStart(), GetTerminalPartialness(), CWriteUtil::GetTrnaAntiCodon(), CEditingActionFeatTranslExcept::GetValue(), HasExcludedAnnotation(), IfOnlyStopCodon(), InheritPartialness(), CLocationEditPolicy::Is5AtEndOfSeq(), CExtendPartialFeatDlg::Is5AtStartOfSeq(), IsContinuous(), IsGeneLocationOk(), IsMixedStrandGeneLocationOk(), CConvertBadCdsAndRnaToMiscFeat::IsNonExtendable(), IsNonExtendable(), IsPartialStartConflict(), MakeCompartments(), CFeatureTableReader::MakeGap(), MakeGeneForFeature(), MakemRNAforCDS(), CMatchmRNA::MatchAnyUnderlyingCDS(), CMatchmRNA::MatchesUnderlyingCDS(), CGtfLocationMerger::MergeLocationForGene(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CMrnaMatchInfo::OkWithoutCds(), CBestFeatFinder::CSeqLocSort::operator()(), PatchTargetSequence(), CValidError_imp::PostErr(), CTabularFormatter_StopCodonChanges::Print(), printed_range(), ProjectExon_newlogic(), variation::CVariationUtil::Remap(), RemapOtherProtFeats(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_AddTopLevelGenomicLinks(), s_BuildMaskedRanges(), s_CheckIntervals(), s_CheckLocationResults(), s_CodonVariation(), s_CoincidingGapFeatures(), s_CompareTwoSeqGraphs(), s_ContainedIn(), s_GetFeatureKeyLinkLocation(), s_GetRestrictedBlastSeqLocs(), s_LocSortCompare(), s_MatchPartialType(), s_OverlapOrAbut(), CFeatureGenerator::s_ProjectRNA(), s_RestrictSeqLocs_Multiframe(), s_ShouldRemoveRef(), s_ShouldSetGenePartialStart(), s_SortShorttRNAs(), SeqLocExtend(), CCleanup::SeqLocExtend(), SeqLocExtend5(), C5ColImportData::Serialize(), CReportEntry::SetAlignment(), CBedFeatureRecord::SetBlocks(), CReportEntry::SetCds(), CGffFeatureRecord::SetLocation(), CFeatureGenerator::SImplementation::SetPartialFlags(), variation_ref::CVariationUtil::SetVariantProperties(), SplitLocationForGap(), StartAbutsGap(), CFeatureGenerator::SImplementation::StitchSmallHoles(), TestOneCDS(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CMacroFunction_LocEnd::TheFunction(), CMacroFunction_LocationDistConstraint::TheFunction(), CCrossRefFeatsDlg::TransferDataToWindow(), TransferPartialness(), CAlignmentAssistant::TranslateLocations(), variation::CVariationUtil::TranslateNAtoAA(), CEditSeqEndsWithAlign::TrimQualityScores(), TrimSeqGraph(), TruncateSeqLoc(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CCleanup::WGSCleanup(), CFeatureItem::x_AddQualsProt(), CSeqTextDataSourceInterval::x_AddVariationsFromFeature(), CEditObjectSeq_feat::x_AdjustCircularGene(), CEditObjectSeq_feat::x_AdjustGene(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CCompareSeq_locs::x_Compare(), CCompareSeq_locs::x_CompareInts(), CSeq_loc::x_CompareSingleId(), CNaSeqlocHelper::x_ComputeSiteIndex(), CCorrectGenesDialog::x_CorrectPairInterval(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CLocation_constraint::x_DoesLocationMatchDistanceConstraint(), CSNPSearchJob::x_DoSearch(), CFeaturePropagator::x_ExtendToStopCodon(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFastaOstreamEx::x_GetCodeBreak(), CObjectIndex::x_GetFeatureCode(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CBioseqIndex::x_InitFeats(), CCDSTranslationProblems::x_Is5AtEndSpliceSiteOrGap(), CSingleFeatValidator::x_IsMostlyNs(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CValidError_bioseq::x_PartialAdjacentToIntron(), variation::CHgvsParser::x_PlacementCoordsToStr(), CFeatureGenerator::SImplementation::x_SetComment(), variation::CVariationUtil::x_SetVariantPropertiesForIntronic(), variation_ref::CVariationUtil::x_SetVariantPropertiesForIntronic(), CSequenceUpdater::x_ShouldRemoveFeature(), CUnorderedSplitter::x_SplitDeltaExt(), IEditingActionFeat::x_TestGeneForFeature(), CFastaOstreamEx::x_TrimLocation(), CVectorTrimPanel::x_TrimSeqGraphData(), CReportTrim::x_TrimSeqGraphData(), CFeaturePropagator::x_TruncateToStopCodon(), CAdjustForConsensusSpliceSite::x_UpdateExonFeatures(), CCreateGeneModelTask::x_UpdateGeneOnSequence(), CValidError_bioseq::x_ValidateAbuttingRNA(), CSingleFeatValidator::x_ValidateGeneXRef(), CValidError_graph::x_ValidateGraphLocation(), CValidError_graph::x_ValidateGraphValues(), CCdregionValidator::x_ValidateParentPartialness(), CValidError_align::x_ValidateStrand(), CGff2Writer::xAssignFeatureEndpoints(), CGff3Writer::xAssignFeatureEndpoints(), CFeatTableEdit::xGetGeneLocation(), CGff3AnnotAssembler::xProcessFeatureCds(), CFeatTableEdit::xPutErrorMissingLocustag(), CFeatTableEdit::xPutErrorMissingProteinId(), CFeatTableEdit::xPutErrorMissingTranscriptId(), and CGff2Record::xUpdateFeatureData().

Definition at line 963 of file Seq_loc.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::GetBond(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CPacked_seqint::GetStop(), CPacked_seqpnt::GetStop(), CSeq_bond::GetStop(), CSeq_interval::GetStop(), CSeq_loc_mix::GetStop(), COpenRange< Position >::GetTo(), COpenRange< TSeqPos >::GetWhole(), kInvalidSeqPos, NCBI_THROW_FMT, CSeq_loc_Base::SelectionName(), and CSeq_loc_Base::Which().

Referenced by AdjustFeatureEnd3(), AdjustGene(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), AdjustMappedStop(), CFeatGapInfo::AdjustProteinSeq(), CSplign::AlignSingleCompartment(), ApplyPolicyToFeature(), BOOST_AUTO_TEST_CASE(), CFeatureIndex::CFeatureIndex(), Check3Extend(), CheckAdjustStartAndStop(), CheckAdjustStop(), variation_ref::CVariationUtil::CheckExonBoundary(), CheckTerminalExceptionResults(), CIdRangeMap::CIdRangeMap(), CMatchFeat::CMatchFeat(), CFeatGapInfo::CollectGaps(), CWriteUtil::CompareFeatures(), CConvertCDSToMiscFeat::Convert(), CVariationNormalizationDelIns::ConvertExpandedDeletionToDelIns(), CCdsToMatPeptide::ConvertInner(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CCleanup::ExpandGeneToIncludeChildren(), CEditSequenceEnds::Extend3(), CExtendPartialFeatDlg::ExtendCDS(), ExtendCDSToStopCodon(), ExtendLocationForTranslExcept(), ExtendStop(), CCleanup::ExtendStopPosition(), ExtendToGapsOrEnds(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), CCleanup::ExtendToStopIfShortAndNotPartial(), CBestFeatFinder::FindBestFeatForLoc(), CInternalStopFinder::FindStartStopRanges(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), FormatAsAsn(), CHTMLFormatterEx::FormatLocation(), CValidError_bioseq::GapByGapInst(), CScore_StartStopCodon::Get(), CScore_CdsScore::Get(), NSnp::GetAlleles(), GetCdRegionCB(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeq_loc::GetCircularLength(), CExtendCDSToStop::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CProteinAlignText::GetGenomicBounds(), CSeq_featHandler::GetLabel(), GetLastCodonLoc(), GetOverlappingFeatures(), CCleanup::GetProteinLocationFromNucleotideLocation(), GetRetranslateCDSCommand(), IRepeatRegion::GetSeqPosEnd(), GetStop(), CSeq_loc_mix::GetStop(), GetTerminalPartialness(), CWriteUtil::GetTrnaAntiCodon(), HasExcludedAnnotation(), IfOnlyStopCodon(), InheritPartialness(), InspectSeqFeat(), CExtendPartialFeatDlg::Is3AtEndOfSeq(), CLocationEditPolicy::Is3AtEndOfSeq(), IsContinuous(), IsExtendable(), IsGeneLocationOk(), IsMixedStrandGeneLocationOk(), CConvertBadCdsAndRnaToMiscFeat::IsNonExtendable(), IsNonExtendable(), IsPartialStopConflict(), CCleanup::LocationMayBeExtendedToMatch(), MakeCompartments(), CFeatureTableReader::MakeGap(), MakeGeneForFeature(), MakemRNAforCDS(), CMatchmRNA::MatchAnyUnderlyingCDS(), CMatchmRNA::MatchesUnderlyingCDS(), CCdsToMatPeptide::MergeConvert(), CGtfLocationMerger::MergeLocationForGene(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CMrnaMatchInfo::OkWithoutCds(), CBestFeatFinder::CSeqLocSort::operator()(), printed_range(), ProjectExon_newlogic(), variation::CVariationUtil::Remap(), RemapOtherProtFeats(), CStd_seg::RemapToLoc(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_AddTopLevelGenomicLinks(), s_CheckIntervals(), s_CheckLocationResults(), s_CoincidingGapFeatures(), s_CompareTwoSeqGraphs(), s_ContainedIn(), variation::CVariationUtil::s_FindLocationProperties(), s_GetFeatureKeyLinkLocation(), s_GetRestrictedBlastSeqLocs(), s_IsLocationEndAtOtherLocationInternalEndpoint(), s_LocSortCompare(), s_MakePointForLocationStop(), s_MatchPartialType(), s_OverlapOrAbut(), s_ParseTRnaFromAnticodonString(), CFeatureGenerator::s_ProjectRNA(), s_RestrictSeqLocs_Multiframe(), s_SeqLocEndsOnBioseq(), s_ShouldRemoveRef(), s_ShouldSetGenePartialStop(), SeqLocExtend(), CCleanup::SeqLocExtend(), SeqLocExtend3(), C5ColImportData::Serialize(), CGffFeatureRecord::SetLocation(), CFeatureGenerator::SImplementation::SetPartialFlags(), SetTranslExcept(), variation_ref::CVariationUtil::SetVariantProperties(), StopAbutsGap(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CMacroFunction_LocEnd::TheFunction(), CMacroFunction_LocationDistConstraint::TheFunction(), CCrossRefFeatsDlg::TransferDataToWindow(), TransferPartialness(), CEditSeqEndsWithAlign::TrimQualityScores(), TrimSeqGraph(), TrimStopsFromCompleteCDS(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CCleanup::WGSCleanup(), CFeatureItem::x_AddQualsProt(), CSeqTextDataSourceInterval::x_AddVariationsFromFeature(), CEditObjectSeq_feat::x_AdjustCircularGene(), CEditObjectSeq_feat::x_AdjustGene(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CCompareSeq_locs::x_Compare(), CCompareSeq_locs::x_CompareInts(), CSeq_loc::x_CompareSingleId(), CNaSeqlocHelper::x_ComputeSiteIndex(), CCorrectGenesDialog::x_CorrectPairInterval(), CLocation_constraint::x_DoesLocationMatchDistanceConstraint(), CImportFeatTable::x_DoImportCDS(), CSNPSearchJob::x_DoSearch(), CFeaturePropagator::x_ExtendToStopCodon(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFastaOstreamEx::x_GetCodeBreak(), CObjectIndex::x_GetFeatureCode(), variation::CVariationUtil::x_GetLiteralAtLoc(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CValidError_bioseq::x_PartialAdjacentToIntron(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation::CVariationUtil::x_SetVariantPropertiesForIntronic(), variation_ref::CVariationUtil::x_SetVariantPropertiesForIntronic(), CSequenceUpdater::x_ShouldRemoveFeature(), CUnorderedSplitter::x_SplitDeltaExt(), IEditingActionFeat::x_TestGeneForFeature(), CVectorTrimPanel::x_TrimSeqGraphData(), CReportTrim::x_TrimSeqGraphData(), CAdjustForConsensusSpliceSite::x_UpdateExonFeatures(), CCreateGeneModelTask::x_UpdateGeneOnSequence(), CValidError_bioseq::x_ValidateAbuttingRNA(), CSingleFeatValidator::x_ValidateGeneXRef(), CValidError_graph::x_ValidateGraphLocation(), CCdregionValidator::x_ValidateParentPartialness(), CGff2Writer::xAssignFeatureEndpoints(), CGff3Writer::xAssignFeatureEndpoints(), CFeatTableEdit::xGetGeneLocation(), CFeatTableEdit::xPutErrorMissingLocustag(), CFeatTableEdit::xPutErrorMissingProteinId(), CFeatTableEdit::xPutErrorMissingTranscriptId(), and CGff2Record::xUpdateFeatureData().

Get the location's strand.

If no strand is set, returns eNa_strand_unknown. If different strands are set in different parts, returns eNa_strand_other. Explicitly set unknown strand is ignored when combined whith plus or minus strand. Examples: not-set = unknown not-set + plus = plus unknown + plus = plus unknown + both = other plus + minus = other

Definition at line 882 of file Seq_loc.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, eNa_strand_both, eNa_strand_unknown, CSeq_loc_Base::GetBond(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CPacked_seqint::GetStrand(), CPacked_seqpnt_Base::GetStrand(), CSeq_bond::GetStrand(), CSeq_interval_Base::GetStrand(), CSeq_loc_mix::GetStrand(), CSeq_point_Base::GetStrand(), CPacked_seqpnt_Base::IsSetStrand(), CSeq_interval_Base::IsSetStrand(), CSeq_point_Base::IsSetStrand(), NCBI_THROW_FMT, CSeq_loc_Base::SelectionName(), and CSeq_loc_Base::Which().

Referenced by AdjustCdregionFrame(), CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CEditSeqEndsWithAlign::AdjustFeatureLocations(), CCDSTranslationPanel::AdjustForStopCodonHyperlinkClicked(), AdjustMappedStop(), CFeatTrim::Apply(), variation::ApplyOffsetFuzz(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CBlastSeqVectorOM::CBlastSeqVectorOM(), CNewCleanup_imp::CdregionFeatBC(), CSeq_loc::ChangeToPackedInt(), CWriteUtil::CompareFeatures(), CSeq_feat::CompareNonLocation(), CConvertCDSToMiscFeat::Convert(), CVariationNormalizationDelIns::ConvertExpandedInsertionToDelIns(), CStdSegHit::CStdSegHit(), CEditSequenceEnds::Extend3(), CEditSequenceEnds::Extend5(), CExtendPartialFeatDlg::ExtendCDS(), ExtendCDSToStopCodon(), ExtendLocationForTranslExcept(), ExtendStop(), CCleanup::ExtendStopPosition(), ExtendToGapsOrEnds(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), CProSplign::FindGlobalAlignment(), CInternalStopFinder::FindStartStopRanges(), FixMixLoc(), FormatAsAsn(), FTASeqLocCheck(), GenelocContained(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), GetCdRegionCB(), CInternalStopFinder::GetCDSNucleotideSequence(), CConvertBadCdsAndRnaToMiscFeat::getCdsOverlap(), CExtendCDSToStop::GetCommand(), CAddFeatureBetweenDlg::GetFeatureLocations(), CAlignmentAssistant::GetFeatures(), GetLastCodonLoc(), GetOverlappingFeatures(), GetOverlappingGene(), CCleanup::GetProteinLocationFromNucleotideLocation(), GetProtRefDescr(), CConvertBadCdsAndRnaToMiscFeat::getRnaOverlap(), CCodingPropensity::GetScore(), CCreateFeat::GetStrand(), CValidError_feat::GetTSACDSOnMinusStrandErrors(), CStdSegHit::HasAlignment(), IfOnlyStopCodon(), InheritPartialness(), CNSeq::Init(), CExtendPartialFeatDlg::Is3AtEndOfSeq(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), CExtendPartialFeatDlg::Is5AtStartOfSeq(), IsGeneLocationOk(), IsNonExtendable(), CSeq_loc::IsReverseStrand(), MakeCompartments(), MakeGeneForFeature(), CCdsToMatPeptide::MergeConvert(), CGtfLocationMerger::MergeLocationForGene(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CAutoDefFeatureClause::OkToGroupUnderByLocation(), operator<<(), SSNP_Info::ParseSeq_feat(), CFeatureTableReader_Imp::ParseTrnaExtString(), PatchTargetSequence(), PreserveTerminalCodons(), CGFFReader::Read(), RemapAlignToLoc(), RetranslateCdregion(), CAutoDefFeatureClause::ReverseCDSClauseLists(), CNewCleanup_imp::RnaFeatBC(), CDemoApp::Run(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_CheckLocationAndStrandResults(), s_CodonVariation(), CMacroFunction_ConvertLocStrand::s_ConvertLocationStrand(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetNeighborhoodLocs(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetStartAndStopCodonsLocs(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetUTRLocs(), s_IsLocationEndAtOtherLocationInternalEndpoint(), s_ParseTRnaFromAnticodonString(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation::CHgvsParser::s_SeqIdToHgvsStr(), s_ShouldBeMerged(), s_SortShorttRNAs(), CAutoDefFeatureClause::SameStrand(), SeqLocExtend(), CCleanup::SeqLocExtend(), SeqLocExtend3(), SeqLocExtend5(), CFeatureSearchJob::SeqLocToString(), CReportEntry::SetAlignment(), CReportEntry::SetCds(), SetTranslExcept(), CEditingActionFeatTranslExcept::SetValue(), CBlastTabular::sx_MineSegment(), TestOneCDS(), CMacroFunction_LocationDistConstraint::TheFunction(), TransferPartialness(), TrimSeqFeat(), TruncateSeqLoc(), TruncateTransSplicedCDSForExtension(), CCleanup::WGSCleanup(), CFeatureItem::x_AddQualsCdregionIdx(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), variation::CHgvsParser::x_AsHgvsExpression(), CValidError_bioseq::x_CheckSingleStrandedRNAViruses(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CCorrectGenesDialog::x_CorrectPairInterval(), CCorrectGenesDialog::x_CorrectPairStrand(), CGFFReader::x_CreateGeneFeatures(), CLocation_constraint::x_DoesLocationMatchDistanceConstraint(), CLocation_constraint::x_DoesStrandMatchConstraint(), CFeatGlyph::x_DrawRuler(), CFeaturePropagator::x_ExtendToStopCodon(), CBlastSeqVectorOM::x_FixStrand(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CClonePlacementGlyph::x_GetCloneEnds(), CFeatTrim::x_GetStartOffset(), CHitMatrixDataSource::x_GoodSeg(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), variation::CVariationUtil::x_InferNAfromAA(), CSeq_align_Mapper_Base::x_Init(), CCDSTranslationProblems::x_Is5AtEndSpliceSiteOrGap(), CSGSeqGraphJob::x_LoadSeqTable(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CMacroFunction_FeatStrandednessConstraint::x_Match(), CValidError_bioseq::x_PartialAdjacentToIntron(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CBioseqContext::x_SetLocation(), CVariationNormalization_base< T >::x_Shift(), IEditingActionFeat::x_TestGeneForFeature(), CCorrectGenesDialog::x_TestGeneForFeature(), CFeatTrim::x_TrimLocation(), CFeaturePropagator::x_TruncateToStopCodon(), CCreateGeneModelTask::x_UpdateGeneOnSequence(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CValidError_bioseq::x_ValidateAbuttingRNA(), CRNAValidator::x_ValidateAnticodon(), CValidError_bioseq::x_ValidateCDSagainstVDJC(), CValidError_graph::x_ValidateGraphLocation(), CCdregionValidator::x_ValidateParentPartialness(), CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk(), CSingleFeatValidator::x_ValidateSeqFeatLoc(), CGff2Writer::xAssignFeatureEndpoints(), CGff3Writer::xAssignFeatureEndpoints(), CGff3Writer::xAssignFeatureStrand(), CFeatTableEdit::xGetGeneLocation(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().

Definition at line 1056 of file Seq_loc.hpp.

References SSeq_loc_CI_RangeInfo::m_Strand, CSeq_loc_CI::x_CheckValid(), and CSeq_loc_CI::x_GetRangeInfo().

Referenced by AdjustFeatureEnd3(), AdjustFeatureEnd5(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), BOOST_AUTO_TEST_CASE(), ConvertSeqLocsToPairwiseAln(), CLocationEditPolicy::Extend3(), CLocationEditPolicy::Extend5(), CFeatureGenePanel::GetLocationForGene(), CSeqUtils::GetMappingInfoFromLocation(), GetStrandForLastInterval(), HasMixedStrands(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), IsMixedStrand(), IsMixedStrandGeneLocationOk(), CSeqUtils::IsSameStrands(), OneIdOneStrand(), CDense_seg::RemapToLoc(), s_CheckAbutting(), s_CreateMappingInfo(), s_IsLocationEndAtOtherLocationInternalEndpoint(), s_PartialAtGapOrNs(), s_PrintLocAsJavascriptArray(), s_SeqLocEndsOnBioseq(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangeInfoMap(), s_SeqLocToTotalRangesInfoMapByStrand(), s_Test_CheckIntervals(), s_TestForOverlapEx(), SeqLocToBioseq(), CAlignmentAssistant::TranslateLocations(), CGuiObjectInfoSeq_feat::x_AddExtraInfo(), CFeatGlyph::x_AdjustFrame(), CSGAlignmentJob::x_CreateFeatGlyph(), CClonePlacementGlyph::x_GetCloneEnds(), CAnnotObject_Less::x_GetExtremes(), CSeq_loc_Mapper_Base::x_GetRangeLength(), CCleanup::x_HasShortIntron(), CSeq_loc_Mapper::x_InitGCSequence(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CFeaturePropagator::x_MapLocation(), and CAnnotObject_Info::x_ProcessAlign().

Definition at line 913 of file Seq_loc.hpp.

References CSeq_loc::kDirtyCache, CSeq_loc::m_TotalRangeCacheFrom, CSeq_loc::m_TotalRangeCacheToOpen, and CSeq_loc::x_UpdateTotalRange().

Referenced by CGBProjectHelper::AddProjectItemsFromRID(), CFeatTrim::Apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CdsTrnaOverlapStr(), CFeatHistogramDS::CFeatHistogramDS(), check_no_overlaps(), CDiscrepancyContext::Compare(), CAnnotCompare::CompareFeats(), Convert_Seq_annot_Seq_loc_TotalRange(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CProteinAlignText::CProteinAlignText(), Does3primerAbutGap(), Does5primerAbutGap(), NSnpAnnot::EstimateSNPCount(), CProSplign::FindGlobalAlignment(), NSearchFeatPanel::GatherFeatures(), CScore_StartStopCodon::Get(), CGnomonEngine::GetAnnot(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), CFeatureGenerator::SImplementation::GetCds(), CSeqUtils::GetCdsMappingInfoFromRna(), CConvertBadCdsAndRnaToMiscFeat::getCdsOverlap(), CSeq_loc::GetCircularLength(), NSnpAnnot::GetGraph_CI(), CTableDataFTable::GetIntValue(), CSeq_featHandler::GetLabel(), NSnp::GetLength(), CSeq_feat_Handle::GetProductTotalRange(), GetProteinWeight(), GetProteinWeights(), CSeq_feat_Handle::GetRange(), CProjectView::GetReflectionInfo(), CConvertBadCdsAndRnaToMiscFeat::getRnaOverlap(), CCodingPropensity::GetScore(), GetTrnaAnticodon(), CViewGraphic::InitView(), CVcfTableView::InitView(), CmRNACDSLinker::LinkByLabelAndLocation(), CAlignedFeatureGraph::NeedTooltip(), CDiscrepancyPanel::OnListClk(), CValidatePanel::OnListItemSelected(), SFeatLengthPredicate::operator()(), SOutsideRange::operator()(), LessThan::operator()(), variation::SFastLocSubtract::operator()(), operator<<(), PatchTargetSequence(), CGFFReader::Read(), CFeatureGenerator::SImplementation::RecomputePartialFlags(), CExtendCDSToStop::ResetGenes(), RestoreModelReadingFrame(), RetrievePartsOfLargeChromosome(), CAlignTabExportJob::Run(), CAgpExportJob::Run(), CDemoApp::Run(), CTestBMApp::Run(), s_CreateObjList(), s_GetAlignmentSpans_Interval(), s_GetFeatureKey(), s_GetRnaMappingLocs(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetUTRLocs(), s_LocationsTouch(), s_LocToRange(), s_Render_SeqFeat(), variation::CVariationUtil::s_ResolveIntronicOffsets(), CSeqGraphicPane::SelectSeqLoc(), CFeatureSearchJob::SeqLocToString(), CValidError_graph::ValidateGraphsOnBioseq(), CValidError_bioseq::ValidateSeqFeatContext(), CLinkUtils::x_AddDbxrefFeatureLinks(), CSGAnnotJob::x_AddGraphToMap(), CGuiObjectInfoSeq_feat::x_AddGroupLocationRows(), CFeatureItem::x_AddQualsProt(), CSequenceSearchJob::x_AddToResults(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CSGAlignStatJob::x_CollectAlignStats(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CFlatGatherer::x_CollectSourceFeatures(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSGFeatureJob::x_CreateCloneFeature(), CSGFeatureJob::x_CreateFeatHist(), CSGFeatureJob::x_CreateFeatSmear(), CGFFReader::x_CreateGeneFeatures(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CComponentSearchJob::x_DoSearch(), CCpgSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CCdsGlyph::x_DrawProtSeqWithMapping(), CSnpJob::x_FetchGraphs(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CClonePlacementGlyph::x_GetCloneEnds(), CObjectIndex::x_GetFeatureCode(), CDisplaySeqalign::x_GetFeatureInfo(), CFeatTrim::x_GetStartOffset(), CAlignedFeatureGraph::x_GetTooltip(), CCreateGeneModelTask::x_Group_By_GeneID(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_align_Mapper_Base::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), CAlignedFeatureGraph::x_Layout(), CAlignmentTrack::x_LoadAlignedSeqFeats(), CSGAlignmentJob::x_LoadAlignmentFeats(), CBatchFeatJob::x_LoadFeatProducts(), CSGSeqGraphJob::x_LoadSeqTable(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeqTextView::x_MergeObjects(), CFeatTableView::x_MergeObjects(), CViewGraphic::x_MergeObjects(), variation_ref::CHgvsParser::x_nuc_inv(), CAlignedFeatureGraph::x_RenderFeature(), CFeatureGenerator::SImplementation::x_SetComment(), CBioseqContext::x_SetLocation(), CReportEntry::x_SetRnaCds(), CFeatTrim::x_TrimTrnaExt(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk(), CSingleFeatValidator::x_ValidateRptUnitRangeVal(), CPolyASiteValidator::x_ValidateSeqFeatLoc(), CPolyASignalValidator::x_ValidateSeqFeatLoc(), CValidError_align::x_ValidateSeqLength(), CGff2Writer::xAssignFeatureAttributePartial(), CGff3Writer::xWriteNucleotideFeature(), and CGff3Writer::xWriteProteinFeature().

Definition at line 422 of file Seq_loc.hpp.

Insert new element before the current one (.

See also

InsertNull()). The strand value eNa_strand_unknown produces strand field not set, If eNa_strand_unknown is expicitly required, call SetStrand().

Definition at line 2777 of file Seq_loc.cpp.

References CSeq_loc_I::CSeq_loc_I(), CSeq_loc_Base::e_Int, COpenRange< Position >::Empty(), eNa_strand_unknown, info, CSeq_loc_CI_Impl::InsertRange(), COpenRange< Position >::IsWhole(), CSeq_loc_CI::m_Impl, CSeq_loc_CI::m_Index, CSeq_loc_CI_Impl::MakeLocInterval(), CSeq_loc_I::x_CheckValidForInsert(), and CSeq_loc_I::x_SetSeq_id_Handle().

Referenced by BOOST_AUTO_TEST_CASE(), FindNewLocations(), and CSeq_loc_I::InsertInterval().

Set of Insert*() methods.

All of them insert new element before the one the iterator points to. If the iterator is at the end of CSeq_loc then the new element is inserted after the last element of the CSeq_loc. After the insertion this iterator will point to the element it was pointing before (or end), and the result iterator will point to the inserted element. All other iterators of the same CSeq_loc object will become invalid. If the insertion point is completely within an equiv set (excluding the equiv set boundary) the equiv set will be expanded appropriately. If the insertion point is completely within an equiv part (excluding the equiv part boundary) the new element is added to that equiv part. If the insertion point is between two equiv parts of the same set then the new element is appended to the part just before the insertion point. The effect of the insertion on equiv sets can be modified by calling SetEquivMode(EEquivMode).

See also

SetEquivMode()

Definition at line 2731 of file Seq_loc.cpp.

References CSeq_loc_I::CSeq_loc_I(), CSeq_loc_Base::e_Null, CSeq_loc_CI_Impl::InsertRange(), CSeq_loc_CI::m_Impl, CSeq_loc_CI::m_Index, and CSeq_loc_I::x_CheckValidForInsert().

Referenced by FindNewLocations().

Insert new element before the current one (.

See also

InsertNull()). The strand value eNa_strand_unknown produces strand field not set, If eNa_strand_unknown is expicitly required, call SetStrand().

Definition at line 2760 of file Seq_loc.cpp.

References CSeq_loc_I::CSeq_loc_I(), CSeq_loc_Base::e_Pnt, eNa_strand_unknown, info, CSeq_loc_CI_Impl::InsertRange(), CSeq_loc_CI::m_Impl, CSeq_loc_CI::m_Index, CSeq_loc_CI_Impl::SetPoint(), CSeq_loc_I::x_CheckValidForInsert(), and CSeq_loc_I::x_SetSeq_id_Handle().

Referenced by CSeq_loc_I::InsertPoint().

Find the intersection with the seq-loc, merge/sort resulting ranges depending on flags.

Return a new seq-loc object.

Definition at line 5183 of file Seq_loc.cpp.

References flags, CSeq_loc::fMerge_SingleRange, CSeq_loc::Subtract(), and tmp.

Referenced by check_no_overlaps(), variation::CVariationUtil::FindLocationProperties(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CBedAnnotAssembler::ProcessRecord(), s_GetTrimmedLength(), s_UpdateCodeBreaksAndAnticodons(), variation::CVariationUtil::TranslateNAtoAA(), TruncateToCDS(), CFeatGapInfo::x_AdjustAnticodons(), CFeatGapInfo::x_AdjustCodebreaks(), variation::CVariationUtil::x_GetLiteralAtLoc(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CRNAValidator::x_ValidateTrnaOverlap(), and CBedReader::xParseFeatureGeneModelFormat().

True if the current location is empty.

Definition at line 1084 of file Seq_loc.hpp.

References COpenRange< Position >::Empty(), SSeq_loc_CI_RangeInfo::m_Range, CSeq_loc_CI::x_CheckValid(), and CSeq_loc_CI::x_GetRangeInfo().

Referenced by CEditSequence::AdjustFeatureLocations(), CEditSequence::AdjustProtFeatureLocations(), CFuseJoinsInLocs::apply(), BOOST_AUTO_TEST_CASE(), ConvertSeqLocsToPairwiseAln(), GetBioseqForSeqFeat(), s_CheckAbutting(), s_ContainsGaps(), s_CreateMappingInfo(), s_NormalizeNullsBetween(), CAlignmentAssistant::TranslateLocations(), CFeatGlyph::x_AdjustFrame(), CFeatGlyph::x_DrawRuler(), IEditingActionFeat::x_GetSublocOnBioseq(), CCleanup::x_HasShortIntron(), CSeq_loc_Mapper::x_InitGCSequence(), and CFeaturePropagator::x_MapLocation().

check start or stop of location for e_Lim fuzz

Definition at line 3222 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, 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::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CPacked_seqint::IsPartialStart(), CPacked_seqpnt::IsPartialStart(), CSeq_interval::IsPartialStart(), CSeq_loc_mix::IsPartialStart(), CSeq_point::IsPartialStart(), and CSeq_loc_Base::Which().

Referenced by CExonFromCds::AddIntron(), CBulkCDSAddPanel::AddOneCmd(), CPartialStartColumn::AddToFeature(), CPartialStopColumn::AddToFeature(), CAutoDefFeatureClause::AddToLocation(), AdjustCdregionFrame(), CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), AdjustFeatureEnd5(), AdjustFeaturePartialFlagForLocation(), CFeatGapInfo::AdjustForRelevantGapIntervals(), AdjustGene(), AdjustProteinFeaturePartialsToMatchCDS(), AdjustProteinMolInfoToMatchCDS(), CFeatTrim::Apply(), CRecomputeIntervals::apply(), CAdjustFeatsForIntrons::apply(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), BOOST_AUTO_TEST_CASE(), CAutoDefParsedClause::CAutoDefParsedClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CNewCleanup_imp::CdRegionEC(), CPartialStartColumn::ClearInFeature(), CPartialStopColumn::ClearInFeature(), CFixForTransSplicing::CombineFeatures(), CFeaturePropagator::ConstructProteinFeatureForPropagatedCodingRegion(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CopyFeaturePartials(), CreateSeqLocMapperFromFeat(), CExtendPartialFeatDlg::ExtendCDS(), ExtendToGapsOrEnds(), ExtendToStopCodon(), CEditingActionFeatGeneLocusPlain::Find(), CEditingActionFeatGeneLocusRna::Find(), CEditingActionFeatGeneLocusCdsGeneProt::Find(), CSeqTranslator::FindBestFrame(), FindNewLocations(), IEditingActionFeat::FindOrCreateProtFeat(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CCleanup::FixRNAEditingCodingRegion(), CGBSeqFormatter::FormatFeature(), CCdsFromGeneMrnaExon::GetCommand(), CExonFromCds::GetCommand(), CExtendCDSToStop::GetCommand(), CFuseFeaturesDlg::GetCommand(), CGeneFeatFromOtherFeatDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CResolveIntersectingFeats::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), CGeneFeatFromXrefs::GetCommand(), GetEditLocationCommand(), CPartialStartColumn::GetFromFeat(), GetLastPartialCodonLength(), CFeatureGenePanel::GetLocationForGene(), CFeatureGenePanel::GetNewGene(), CCleanup::GetProteinLocationFromNucleotideLocation(), GetProtRefAnnot(), GetProtRefDescr(), GetTerminalPartialness(), HasBadStartCodon(), InheritPartialness(), CLocationEditPolicy::Interpret5Policy(), IsExtendable(), IsGeneLocationOk(), IsLocationInFrame(), CConvertBadCdsAndRnaToMiscFeat::IsNonExtendable(), IsNonExtendable(), CAutoDefFeatureClause::IsPartial(), CSeqUtils::IsPartialStart(), CSeq_loc_mix::IsPartialStart(), IsPartialStartConflict(), MakeGeneForFeature(), MakemRNAforCDS(), CCdsToMatPeptide::MergeConvert(), PartialsSame(), CFeaturePropagator::Propagate(), RemapOtherProtFeats(), CNewCleanup_imp::ResynchPeptidePartials(), CNewCleanup_imp::ResynchProteinPartials(), RetranslateCdregion(), s_CheckLocationResults(), s_FixPartial(), s_GetCdsByLocation(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetStartAndStopCodonsLocs(), s_ShouldSetGenePartialStart(), s_UpdatePartialness(), SeqLocExtend(), CCleanup::SeqLocExtend(), SeqLocExtend5(), CCleanup::SetCDSPartialsByFrameAndTranslation(), CCleanup::SetFrameFromLoc(), CFeatureGenerator::SImplementation::SetPartialFlags(), CSeq_loc::SetPartialStart(), SetProteinFeature(), CMacroFunction_ApplyCDS::TheFunction(), CMacroFunction_LocPartialTest::TheFunction(), TransferPartialness(), CSeqTranslator::Translate(), TranslateCDSCommand(), CSeqTranslator::TranslateToProtein(), TruncateCDSAtStop(), CTruncateCDS::TruncateProteinFeat(), TruncateSeqLoc(), UpdateFeat(), CIntronValidator::Validate(), CValidError_bioseq::ValidateRawConst(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CFeatureTableReader_Imp::x_AddIntervalToFeature(), CFeatureItem::x_AddQualsProt(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CFeaturePropagator::x_CdsCleanupPartials(), CConvertFeatureBase::x_ConvertToCDS(), CCorrectGenesDialog::x_CorrectPairInterval(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CLocation_constraint::x_DoesLocationMatchPartialnessConstraint(), CImportFeatTable::x_DoImportCDS(), CNewCleanup_imp::x_ExtendFeatureToCoverSequence(), CFtableFormatter::x_FormatLocation(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CEditObjectSeq_feat::x_HandleCdsProduct(), CIntronValidator::x_IsIntronShort(), CPromote::x_MakeMolinfoDesc(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CSequenceUpdater::x_MappedFeature_ChangeId(), CSequenceUpdater::x_MappedFeature_ThroughAlign(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CValidError_bioseq::x_PartialAdjacentToIntron(), CPromote::x_PromoteCdregion(), CReportTrim::x_RetranslateCDS(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), CSequenceUpdater::x_RetranslateOldCDSProduct(), CFeatureGenerator::SImplementation::x_SetComment(), CSeq_loc_Mapper_Base::x_StripExtraneousFuzz(), CCreateGeneModelTask::x_UpdateGeneOnSequence(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CValidError_bioseq::x_ValidateAbuttingRNA(), CCdregionValidator::x_ValidateCDSPartial(), CCdregionValidator::x_ValidateParentPartialness(), and CGff3Writer::xAssignFeatureEndpoints().

Definition at line 3251 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, 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::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CPacked_seqint::IsPartialStop(), CPacked_seqpnt::IsPartialStop(), CSeq_interval::IsPartialStop(), CSeq_loc_mix::IsPartialStop(), CSeq_point::IsPartialStop(), and CSeq_loc_Base::Which().

Referenced by CExonFromCds::AddIntron(), CBulkCDSAddPanel::AddOneCmd(), CPartialStartColumn::AddToFeature(), CPartialStopColumn::AddToFeature(), CAutoDefFeatureClause::AddToLocation(), CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), AdjustFeatureEnd3(), AdjustFeaturePartialFlagForLocation(), CFeatGapInfo::AdjustForRelevantGapIntervals(), AdjustGene(), AdjustMappedStop(), AdjustProteinFeaturePartialsToMatchCDS(), AdjustProteinMolInfoToMatchCDS(), CFeatTrim::Apply(), CRecomputeIntervals::apply(), CAdjustFeatsForIntrons::apply(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), BOOST_AUTO_TEST_CASE(), CAutoDefParsedClause::CAutoDefParsedClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CNewCleanup_imp::CdRegionEC(), CPartialStartColumn::ClearInFeature(), CPartialStopColumn::ClearInFeature(), CFixForTransSplicing::CombineFeatures(), CFeaturePropagator::ConstructProteinFeatureForPropagatedCodingRegion(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CopyFeaturePartials(), CExtendPartialFeatDlg::ExtendCDS(), ExtendToGapsOrEnds(), CEditingActionFeatGeneLocusPlain::Find(), CEditingActionFeatGeneLocusRna::Find(), CEditingActionFeatGeneLocusCdsGeneProt::Find(), CSeqTranslator::FindBestFrame(), FindNewLocations(), IEditingActionFeat::FindOrCreateProtFeat(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CGBSeqFormatter::FormatFeature(), CScore_StartStopCodon::Get(), CScore_CdsInternalStops::Get(), CInternalStopFinder::GetCDSNucleotideSequence(), CCdsFromGeneMrnaExon::GetCommand(), CExonFromCds::GetCommand(), CExtendCDSToStop::GetCommand(), CFuseFeaturesDlg::GetCommand(), CGeneFeatFromOtherFeatDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CResolveIntersectingFeats::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), CGeneFeatFromXrefs::GetCommand(), GetEditLocationCommand(), CPartialStopColumn::GetFromFeat(), CFeatureGenePanel::GetLocationForGene(), CFeatureGenePanel::GetNewGene(), CCleanup::GetProteinLocationFromNucleotideLocation(), GetProtRefAnnot(), GetProtRefDescr(), GetTerminalPartialness(), InheritPartialness(), CLocationEditPolicy::Interpret3Policy(), IsExtendable(), IsGeneLocationOk(), IsLocationInFrame(), CConvertBadCdsAndRnaToMiscFeat::IsNonExtendable(), IsNonExtendable(), CAutoDefFeatureClause::IsPartial(), CSeqUtils::IsPartialStop(), CSeq_loc_mix::IsPartialStop(), IsPartialStopConflict(), MakeGeneForFeature(), MakemRNAforCDS(), CCdsToMatPeptide::MergeConvert(), PartialsSame(), CTabularFormatter_StopCodonChanges::Print(), CFeaturePropagator::Propagate(), RemapOtherProtFeats(), CNewCleanup_imp::ResynchPeptidePartials(), CNewCleanup_imp::ResynchProteinPartials(), RetranslateCdregion(), s_CheckLocationResults(), s_FixPartial(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetStartAndStopCodonsLocs(), s_ShouldSetGenePartialStop(), s_UpdatePartialness(), SeqLocExtend(), CCleanup::SeqLocExtend(), SeqLocExtend3(), CCleanup::SetCDSPartialsByFrameAndTranslation(), CCleanup::SetFrameFromLoc(), CFeatureGenerator::SImplementation::SetPartialFlags(), CSeq_loc::SetPartialStop(), SetProteinFeature(), SetTranslExcept(), CMacroFunction_ApplyCDS::TheFunction(), CMacroFunction_LocPartialTest::TheFunction(), TransferPartialness(), CSeqTranslator::Translate(), TranslateCDSCommand(), TrimStopsFromCompleteCDS(), TruncateSeqLoc(), UpdateFeat(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CFeatureTableReader_Imp::x_AddIntervalToFeature(), CFeatureItem::x_AddQualsProt(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CFeaturePropagator::x_CdsCleanupPartials(), CConvertFeatureBase::x_ConvertToCDS(), CCorrectGenesDialog::x_CorrectPairInterval(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CLocation_constraint::x_DoesLocationMatchPartialnessConstraint(), CImportFeatTable::x_DoImportCDS(), CFtableFormatter::x_FormatLocation(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CEditObjectSeq_feat::x_HandleCdsProduct(), CPromote::x_MakeMolinfoDesc(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CSequenceUpdater::x_MappedFeature_ChangeId(), CSequenceUpdater::x_MappedFeature_ThroughAlign(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CValidError_bioseq::x_PartialAdjacentToIntron(), CPromote::x_PromoteCdregion(), CReportTrim::x_RetranslateCDS(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), CSequenceUpdater::x_RetranslateOldCDSProduct(), CSeq_loc_Mapper_Base::x_SetLastTruncated(), CSeq_loc_Mapper_Base::x_StripExtraneousFuzz(), CCreateGeneModelTask::x_UpdateGeneOnSequence(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CValidError_bioseq::x_ValidateAbuttingRNA(), CCdregionValidator::x_ValidateParentPartialness(), and CGff3Writer::xAssignFeatureEndpoints().

Return true if all ranges have reverse strand.

Definition at line 995 of file Seq_loc.hpp.

References CSeq_loc::GetStrand(), and IsReverse().

Referenced by BOOST_AUTO_TEST_CASE(), CdsTrnaOverlapStr(), CSeq_loc_CI_Impl::CSeq_loc_CI_Impl(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CSeq_loc::GetCircularLength(), CmRNAFromGeneCdsExon::GetCommand(), IRepeatRegion::IsReverseStrand(), MakemRNAforCDS(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), and CSeq_loc_Mapper_Base::x_InitializeLocs().

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

Definition at line 858 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::GetBond(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CPacked_seqint::IsSetStrand(), CSeq_bond::IsSetStrand(), CSeq_loc_mix::IsSetStrand(), CPacked_seqpnt_Base::IsSetStrand(), CSeq_interval_Base::IsSetStrand(), CSeq_point_Base::IsSetStrand(), and CSeq_loc_Base::Which().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), CSeq_loc::ChangeToPackedInt(), CFeatGapInfo::CollectGaps(), CWriteUtil::CompareFeatures(), CExtendPartialFeatDlg::ExtendCDS(), ExtendCDSToStopCodon(), CCleanup::ExtendStopPosition(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), FixMixLoc(), GetCdRegionCB(), CExtendCDSToStop::GetCommand(), GetOverlappingFeatures(), IfOnlyStopCodon(), CGtfLocationMerger::MergeLocationForGene(), CMacroFunction_ConvertLocStrand::s_ConvertLocationStrand(), s_IsLocationEndAtOtherLocationInternalEndpoint(), s_ParseTRnaFromAnticodonString(), CNewCleanup_imp::SeqLocBC(), SeqLocExtend3(), SeqLocExtend5(), CEditingActionFeatTranslExcept::SetValue(), TruncateSeqLoc(), TruncateTransSplicedCDSForExtension(), CCleanup::WGSCleanup(), CFeatureItem::x_AddQualsCdregionIdx(), CLocation_constraint::x_DoesLocationMatchDistanceConstraint(), CFeaturePropagator::x_ExtendToStopCodon(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CClonePlacementGlyph::x_GetCloneEnds(), CFeaturePropagator::x_MapLocation(), CVariationNormalization_base< T >::x_Shift(), CFeaturePropagator::x_TruncateToStopCodon(), CValidError_bioseq::x_ValidateAbuttingRNA(), CValidError_bioseq::x_ValidateCDSagainstVDJC(), CCdregionValidator::x_ValidateParentPartialness(), CSingleFeatValidator::x_ValidateSeqFeatLoc(), and CGtfWriter::xAssignFeaturesTranscript().

Get strand.

Definition at line 1049 of file Seq_loc.hpp.

References SSeq_loc_CI_RangeInfo::m_IsSetStrand, CSeq_loc_CI::x_CheckValid(), and CSeq_loc_CI::x_GetRangeInfo().

Referenced by AdjustFeatureEnd3(), AdjustFeatureEnd5(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), BOOST_AUTO_TEST_CASE(), CLocationEditPolicy::Extend5(), CSeqUtils::GetMappingInfoFromLocation(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), OneIdOneStrand(), s_CreateMappingInfo(), s_IsLocationEndAtOtherLocationInternalEndpoint(), s_PrintLocAsJavascriptArray(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangesInfoMapByStrand(), CFeatGlyph::x_AdjustFrame(), CClonePlacementGlyph::x_GetCloneEnds(), CAnnotObject_Less::x_GetExtremes(), CCleanup::x_HasShortIntron(), and CSeq_loc_Mapper::x_InitGCSequence().

check if parts of the seq-loc are missing

Definition at line 3346 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CPacked_seqint::IsTruncatedStart(), CPacked_seqpnt::IsTruncatedStart(), CSeq_interval::IsTruncatedStart(), CSeq_loc_mix::IsTruncatedStart(), CSeq_point::IsTruncatedStart(), and CSeq_loc_Base::Which().

Referenced by CreateSeqLocMapperFromFeat(), InheritPartialness(), CSeq_loc_mix::IsTruncatedStart(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetStartAndStopCodonsLocs(), CSeq_loc::SetTruncatedStart(), and TransferPartialness().

Definition at line 3372 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CPacked_seqint::IsTruncatedStop(), CPacked_seqpnt::IsTruncatedStop(), CSeq_interval::IsTruncatedStop(), CSeq_loc_mix::IsTruncatedStop(), CSeq_point::IsTruncatedStop(), and CSeq_loc_Base::Which().

Referenced by InheritPartialness(), CSeq_loc_mix::IsTruncatedStop(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetStartAndStopCodonsLocs(), CSeq_loc::SetTruncatedStop(), and TransferPartialness().

Definition at line 410 of file Seq_loc.hpp.

Create equiv set with one part from current position to the position pointed by end_it argument exclusive.

The end_it position must be after current position. If there are any conflicts with existing equiv sets or bond pairs no new equiv set will be made and an exception will be thrown. New set's level will be assigned depending on its size in relation to existing overlapping equiv sets.

Create equiv set with one part from current position to the position pointed by end_it argument exclusive.

The end_it position must be after current position. If there are any conflicts with existing equiv sets or bond pairs no new equiv set will be made and an exception will be thrown.

return constructed CSeq_loc with all changes

Definition at line 2946 of file Seq_loc.cpp.

References CSeq_loc_CI::m_Impl, and CSeq_loc_CI_Impl::MakeLoc().

Referenced by CEditSequence::AdjustFeatureLocations(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), CEditSequence::AdjustProtFeatureLocations(), CFuseJoinsInLocs::apply(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), FindNewLocations(), CSequenceUpdater::s_OffsetLocation(), CAlignmentAssistant::TranslateLocations(), UpdateToBestId(), CFeatGlyph::x_AdjustFrame(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CFeatGlyph::x_DrawRuler(), IEditingActionFeat::x_GetSublocOnBioseq(), and CFeaturePropagator::x_MapLocation().

All functions create and return a new seq-loc object.

Optional synonym mapper may be provided to detect and convert synonyms of a bioseq. Length getter is used by Subtract() to calculate real sequence length. Merge ranges depending on flags, return a new seq-loc object.

Definition at line 5037 of file Seq_loc.cpp.

References flags, CSeq_loc::fMerge_SingleRange, CSeq_loc::fSort, x_MergeAndSort(), x_MergeNoSort(), and x_SingleRange().

Referenced by CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CInternalStopFinder::FindStartStopRanges(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CSeqUtils::GetCdsMappingInfoFromRna(), GetRelatedFeatureApplyObjects(), CSeq_loc_Mapper_Base::MapTotalRange(), CGff3LocationMerger::MergeLocation(), CGtfLocationMerger::MergeLocationDefault(), CGtfLocationMerger::MergeLocationForCds(), CGtfLocationMerger::MergeLocationForGene(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CBedAnnotAssembler::ProcessRecord(), s_CombineDustMasksWithUserProvidedMasks(), variation_ref::CVariationUtil::s_FactorOutLocsInPlace(), Seq_loc_Merge(), CSGAlignmentJob::x_CreateFeatGlyph(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), IEditingActionFeat::x_GetSublocOnBioseq(), and CFeaturePropagator::x_MapLocation().

Remove equiv set, all pieces that are part of the set will be preserved as independent pieces.

Reset the strand on this location.

Definition at line 5221 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CPacked_seqint::ResetStrand(), CPacked_seqpnt_Base::ResetStrand(), CSeq_interval_Base::ResetStrand(), CSeq_loc_mix::ResetStrand(), CSeq_point_Base::ResetStrand(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().

Referenced by CCompareSeq_locs::CCompareSeq_locs(), CFeatGapInfo::CollectGaps(), variation::Contains(), CCleanup::GetProteinLocationFromNucleotideLocation(), CNewCleanup_imp::SeqLocBC(), TestDoNotExtendOverGap(), TestMapper_Trimming(), CCorrectGenesDialog::x_CorrectPairStrand(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), and x_ToBlastVec().

Definition at line 989 of file Seq_loc.hpp.

Referenced by CSeq_loc_Conversion::ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), GetSPSeqLoc(), MakeBond(), CSeq_loc_CI_Impl::MakeLocBond(), ReverseComplementLocation(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), SeqLocPrintUseBestID(), UpgradeSeqLocId(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CSeq_loc_CI_Impl::x_CreateBond(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().

Definition at line 981 of file Seq_loc.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CTestObjMgr::CreateEmptySSeqLoc(), CSeq_loc_Conversion::GetDstId(), CSeq_loc_Conversion::MakeDstMix(), CSeq_loc_CI_Impl::MakeLocOther(), SCigarAlignment::operator()(), s_CreateStdSegs(), s_OOFBlastHSP2SeqAlign(), CClippedScorer::ScoreAlignments(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CAnnot_Collector::x_CollectSegments(), CCompareSeq_locs::x_ComputeOverlapValues(), CSeq_align_Mapper_Base::x_GetDstStd(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), variation_ref::CHgvsParser::x_identity(), variation_ref::CHgvsParser::x_location(), x_PushRange(), CSeq_loc_Mapper_Base::x_PushSourceRange(), variation::CVariationUtil::x_Remap(), CAnnot_Collector::x_SearchRange(), CAnnot_Collector::x_SearchSegments(), CWig2tableApplication::x_SetTotalLoc(), CAlnSpanVertModel::x_UpdateLocs(), and CWiggleReader::xSetTotalLoc().

Definition at line 988 of file Seq_loc.hpp.

Referenced by CSeq_loc_Conversion::ConvertEquiv(), CSeq_loc_Conversion_Set::ConvertEquiv(), CSeq_loc_CI_Impl::MakeLoc(), CSeq_loc_Mapper_Base::Map(), NormalizeLoc(), ReverseComplementLocation(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), SplitLocationForGap(), UpgradeSeqLocId(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and xgbloc_ver().

Set the range from position.

Definition at line 2818 of file Seq_loc.cpp.

References info, CSeq_loc_CI::m_Impl, CSeq_loc_CI_Impl::UpdateLoc(), CSeq_loc_CI::x_CheckValid(), and CSeq_loc_I::x_GetRangeInfo().

Referenced by CEditSequence::AdjustFeatureLocations(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), CEditSequence::AdjustProtFeatureLocations(), CFuseJoinsInLocs::apply(), CSequenceUpdater::s_OffsetLocation(), CAlignmentAssistant::TranslateLocations(), CFeatGlyph::x_AdjustFrame(), CFeatGlyph::x_DrawRuler(), and CFeaturePropagator::x_MapLocation().

set the 'id' field in all parts of this location

Definition at line 3474 of file Seq_loc.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_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, ERR_POST_X, Error(), CSeq_loc_Base::GetBond(), CSeq_loc::InvalidateCache(), NON_CONST_ITERATE, CSeq_bond_Base::SetA(), CSeq_bond_Base::SetB(), CSeq_loc::SetBond(), CSeq_loc::SetEmpty(), CSeq_loc::SetEquiv(), CPacked_seqpnt_Base::SetId(), CSeq_interval_Base::SetId(), CSeq_point_Base::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CSeq_loc::SetWhole(), and CSeq_loc_Base::Which().

Referenced by CFeatGapInfo::AdjustProteinSeq(), BOOST_AUTO_TEST_CASE(), CFastaSeqBlockItem::CFastaSeqBlockItem(), CFlatFileTextItem::CFlatFileTextItem(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CCreateProteinId::create_protein_ids(), FinalCleanup(), CFlatAnticodonQVal::Format(), GetProductLabel(), GetRetranslateCDSCommand(), CAlignSpanView::GetSelection(), CAlignGlyph::GetSignature(), CSeqTextWidget::GetVisibleRange(), CCrossAlignView::GetVisibleRanges(), CDotMatrixView::GetVisibleRanges(), CViewGraphic::GetVisibleRanges(), CNSeq::Init(), CFastaObjectLoader::LoadFromStream(), CIdMapper::Map(), CCdsToMatPeptide::MergeConvert(), variation_ref::CVariationUtil::PrecursorToProt(), CSeedTop::Run(), s_AddCoalescedLocations(), s_AddSitesToAnnot(), s_CombineRefs(), s_ConvertToBlastQueries(), s_CreateKmerCounts(), s_RemapFeatureSeqIds(), s_Seq_align_Seq_loc(), CPsiBlastTestFixture::s_SetupSubject(), CSeq_loc::SetId(), CGeneFinder::CGeneSearchPlugin::setUpFeatureIterator(), sProductFromString(), CAlignmentAssistant::TranslateLocations(), variation::CVariationUtil::TranslateNAtoAA(), TruncateSeqLoc(), CBlastDB_FastaFormatter::Write(), CFastaExportJob::x_CheckForDuplicates(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFindITSParser::x_CreateMiscRna(), CSGAlignStatJob::x_CreatePileUpGraphs(), CNGAlignJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CFindITSParser::x_CreateRRna(), CComponentSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CFeatGlyph::x_DrawRuler(), CFastaExportJob::x_GetWholeLoc(), CSGAlignmentJob::x_LoadAlignmentFeats(), CBatchFeatJob::x_LoadFeatProducts(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CSequenceUpdater::x_MappedFeature_ChangeId(), CReportEntry::x_MapPos(), CSeqTextView::x_MergeObjects(), CFeatTableView::x_MergeObjects(), CViewGraphic::x_MergeObjects(), CFeatTableView::x_PreAttachToProject(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CPsiBl2SeqTestFixture::x_SetupSubject(), CFeaturePropagator::x_TruncateToStopCodon(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CModifySeqId::x_UpdateLoc(), CAlnSpanVertModel::x_UpdateLocs(), and CFeatTableEdit::xGetGeneLocation().

Definition at line 983 of file Seq_loc.hpp.

Referenced by AddCdregionToSmallGenomeSet(), CSeq_loc_mix::AddInterval(), CExonFromCds::AddIntron(), variation_ref::CVariationUtil::AdjustDelinsToInterval(), AgpRead(), CConvertRptUnitRangeToLoc::apply(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), variation::ApplyOffsetFuzz(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), BuildGoodSpliceNucProtSet(), Canonicalize(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CCompareSeqRegions::CCompareSeqRegions(), CFastaSeqBlockItem::CFastaSeqBlockItem(), CFlatFileTextItem::CFlatFileTextItem(), CSeq_loc::ChangeToMix(), Check3Policy(), CObjMgr_QueryFactory::CObjMgr_QueryFactory(), CollapseDiscontinuitiesInUTR(), CConvertCDSToMiscFeat::Convert(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CNewCleanup_imp::ConvertSeqLocWholeToInt(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CTestObjMgr::CreateBlastSearchQuery(), CreateFeatLocation(), CAlignmentAssistant::CreateFeature(), CEditSequence::CreateFeature(), variation_ref::CVariationUtil::CreateFlankLocs(), variation::CVariationUtil::CreateFlankLocs(), CreateLoc(), CreateOrderedLoc(), CEditSequence::CreateRegulatory(), CSeq_align::CreateRowSeq_loc(), CSeqUtils::CreateSeq_loc(), CreateTwoIntLoc(), CGBObjectLoader::Execute(), ExtendCDSToStopCodon(), ExtendLocationForTranslExcept(), ExtendStop(), CCleanup::ExtendStopPosition(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), CdBlaster::FillOutSeqLoc(), CSimpleB2SWrapper::FillOutSeqLoc(), CBestFeatFinder::FindBestFeatForLoc(), variation::FindSSRLoc(), CInternalStopFinder::FindStartStopRanges(), FormatAsAsn(), fta_get_seqloc_int_whole(), SSeqTableContent::GetAnnot(), CVDBGraphSeqIterator::GetAnnot(), CInternalStopFinder::GetCDSNucleotideSequence(), CAddGlobalCodeBreak::GetCommand(), CExonFromCds::GetCommand(), CExtendCDSToStop::GetCommand(), CProteinAlignText::GetGenomicBounds(), GetGoodSeqEntryWithFeatureIds(), CHistogramGlyph::GetHTMLActiveAreas(), GetLastCodonLoc(), CGtfLocationRecord::GetLocation(), CBulkLocationPanel::GetLocForBioseq(), GetRandomSegment(), CBioseq_Handle::GetRangeSeq_loc(), GetRetranslateCDSCommand(), CCodingPropensity::GetScore(), CAlignSpanView::GetSelection(), CSNPDbFeatIterator::GetSeq_feat(), CLocationListCtrl::GetSeq_loc(), CGffBaseColumns::GetSeqLoc(), GetSeqLocIntSP(), GetSPSeqLoc(), CSeqTextWidget::GetVisibleRange(), CCrossAlignView::GetVisibleRanges(), CDotMatrixView::GetVisibleRanges(), CViewGraphic::GetVisibleRanges(), HasExcludedAnnotation(), CGtfImportData::Initialize(), C5ColImportData::Initialize(), CBedImportData::Initialize(), IsGeneLocationOk(), CFastaObjectLoader::LoadFromStream(), MakeCLoc(), MakeDDFromSeqLoc(), CSeq_loc_Conversion::MakeDstMix(), MakeEntryForDeltaConversion(), MakeInterval(), CSeq_loc_CI_Impl::MakeLocInterval(), MakeMixLoc(), MakeMultiSeqCDS(), MakeSeqLocFromDD(), CLocMapper_Default::Map(), CGtfLocationMerger::MergeLocationForGene(), CSeqUtils::MixLocToLoc(), NormalizeLoc(), CStd_seg::OffsetRow(), CAlignmentAssistant::OnAddAlignCDS(), CAlignmentAssistant::OnAddAlignOther(), CAlignmentAssistant::OnAddAlignRNA(), CAgpToSeqEntry::OnGapOrComponent(), CRepeatMaskerReader::ParseRecord(), ProjectAndCollapseCDS(), ProjectExon_newlogic(), ProjectExon_oldlogic(), CStd_seg::RemapToLoc(), SRelLoc::Resolve(), RevComp(), ReverseComplementLocation(), CXcompareAnnotsApplication::Run(), CDemoApp::Run(), CFeatTreeSampleApp::Run(), CSampleObjmgrApplication::Run(), CTestSingleAln_All::RunTest(), s_AddCoalescedLocations(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_AddSitesToAnnot(), s_ConvertToBlastQueries(), CSeq_loc_Conversion::s_ConvertToMix(), s_ConvertWholeToInt(), s_CoverageSeqLoc(), s_CreateStdSegs(), s_FixIntervalProtToCds(), s_FlattenLoc(), s_GetCdregionPlusUpstream(), s_GetMaskLoc(), s_GetPolyA_genomic_priming(), s_GetUngapLoc(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetUTRLocs(), s_HasMobileElementForInterval(), s_MakeMixLoc(), s_MakeSliceMapper(), s_OOFBlastHSP2SeqAlign(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), s_Seq_align_Seq_loc(), s_SeqLocDelete(), s_SeqMapForHandle(), s_SetSplitQuerySeqInterval(), sConvertIntToPoint(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CNewCleanup_imp::SeqLocBC(), CSeq_loc_Conversion::SetDstLoc(), CSeqTableSetLocFuzzFromLim::SetInt(), CSeqTableSetLocFuzzToLim::SetInt(), CGffFeatureRecord::SetLocation(), SetNewInterval(), CGeneFinder::CGeneSearchPlugin::setUpFeatureIterator(), SimpleSeqLocFromBioseq(), SplitLocationForGap(), StartAbutsGap(), StopAbutsGap(), CReadBlastApp::StoreBlast(), TestFuseAbuttingIntervals(), TestOneCDS(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestTwoIntCdsFromLastBioseqOutsideAlign(), CSingleCDSExceptionPanel::TransferDataFromWindow(), variation::CVariationUtil::TranslateNAtoAA(), TruncateSeqLoc(), TruncateToCDS(), TruncateTransSplicedCDSForExtension(), TryOneCaseMixLoc(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), UpgradeSeqLocId(), CPhrap_Contig::x_AddBaseSegFeats(), CFeatureTableReader_Imp::x_AddIntervalToFeature(), CMultiAligner::x_AddNewSegment(), CPhrap_Read::x_AddQualityFeat(), CPhrap_Contig::x_AddReadLocFeats(), CPhrap_Read::x_AddTagFeats(), CPhrap_Contig::x_AddTagFeats(), CEditObjectSeq_feat::x_AdjustCircularGene(), variation::CVariationUtil::x_AdjustDelinsToInterval(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CCorrectGenesDialog::x_CorrectPairInterval(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFindITSParser::x_CreateMiscRna(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CSGAlignStatJob::x_CreatePileUpGraphs(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CProSplignJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CFindITSParser::x_CreateRRna(), CComponentSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CSeqMap::x_DoUpdateSeq_inst(), CFeaturePropagator::x_ExtendToStopCodon(), CBlastFastaInputSource::x_FastaToSeqLoc(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CSeq_align_Mapper_Base::x_GetDstStd(), CAutoDef::x_GetFeatureClauses(), CLocationListCtrl::x_GetInterval(), variation::CVariationUtil::x_GetLiteralAtLoc(), CAsn2FlatApp::x_GetLocation(), CFlatFileGenerator::x_GetLocation(), CSraInputSource::x_GetNextSeq_loc(), CEditingBtnsPanel::x_GetSelectedLocations(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), variation::CVariationUtil::x_InferNAfromAA(), CBioseqIndex::x_InitFeats(), variation_ref::CHgvsParser::x_InstToString(), CSGAlignmentJob::x_LoadAlignmentFeats(), CBatchFeatJob::x_LoadFeatProducts(), CVDBGraphSeqIterator::x_MakeTable(), CFeatureGenerator::SImplementation::x_MapFeature(), IEditingActionFeat::x_MergeFeatureLocation(), CSeqTextView::x_MergeObjects(), CFeatTableView::x_MergeObjects(), CViewGraphic::x_MergeObjects(), SCigarAlignment::x_NextChunk(), x_NonTranslatedHSPToStdSeg(), CGFFReader::x_ParseAlignRecord(), CCoiledCoil::x_PredictRegions(), CGenBankLoadOptionPanel::x_ProccessText(), CXcompareAnnotsApplication::x_ProcessMappingRange(), CXcompareAnnotsApplication::x_ProcessMappingRanges(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), variation_ref::CVariationUtil::x_ProtToPrecursor(), x_PushRange(), CSeq_loc_Mapper_Base::x_PushSourceRange(), variation_ref::CHgvsParser::x_range(), CSeq_loc_Mapper_Base::x_RangeToSeq_loc(), CSplitQueryTestFixture::x_ReadQueryBoundsPerChunk(), variation::CVariationUtil::x_Remap(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CGFFReader::x_ResolveLoc(), CVectorTrimPanel::x_SeqLocDelete(), CCDSTranslationPanel::x_SetLocationForProtein(), CWig2tableApplication::x_SetTotalLoc(), x_SingleRange(), variation_ref::CHgvsParser::x_ssr(), CFeaturePropagator::x_TruncateToStopCodon(), x_UngappedHSPToStdSeg(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CAlnSpanVertModel::x_UpdateLocs(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), CGvfReader::xFeatureSetLocationInterval(), XGapToSeqLocEx(), CFeatTableEdit::xGetGeneLocation(), CGff3LocationMerger::xGetRecordLocation(), CUCSCRegionReader::xParseFeatureUCSCFormat(), and CWiggleReader::xSetTotalLoc().

Definition at line 987 of file Seq_loc.hpp.

Referenced by AddInsertWithGaps(), AddLoc(), CSeq_loc_mix::AddSeqLoc(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CCleanup::ClearInternalPartials(), CollapseDiscontinuitiesInUTR(), CSeq_loc::Compare(), CSeq_loc_Conversion_Set::ConvertMix(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CLocationEditPolicy::ConvertToJoin(), CLocationEditPolicy::ConvertToOrder(), CorrectIntervalOrder(), CreateOrderedLoc(), CSeq_align::CreateRowSeq_loc(), CreateTwoIntLoc(), CCleanup::ExtendStopPosition(), CBlastDBExtractor::ExtractFasta(), variation::FindSSRLoc(), CGeneFinder::GeneSearchNormalizeLoc(), CFeatureGenePanel::GetLocationForGene(), CValidError_bioseq::GetLocFromSeq(), CAsn2FastaApp::HandleSeqEntry(), MakeCLoc(), CSeq_loc_CI_Impl::MakeLoc(), MakeMixLoc(), CFeaturePropagator::MakeOrdered(), CLocMapper_Default::Map(), CGencollIdMapper::Map(), CGff3LocationMerger::MergeLocation(), CGtfLocationMerger::MergeLocationDefault(), CGtfLocationMerger::MergeLocationForCds(), CGtfLocationMerger::MergeLocationForGene(), CCompareSeqRegions::NextComparisonGroup(), NormalizeLoc(), PreserveTerminalCodons(), ProjectExons(), RevComp(), ReverseComplementLocation(), CSeq_loc_Conversion::s_ConvertToMix(), s_CoverageSeqLoc(), s_FlattenLoc(), s_GetCdregionPlusUpstream(), s_GetCodeBreakSeqLocMix(), s_GetMaskSeqLoc(), s_MakeMixLoc(), s_NormalizeNullsBetween(), s_SeqLocDelete(), s_TitleFromSegment(), CInvertProcess::SeqEntryProcess(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CNewCleanup_imp::SeqLocBC(), CSeq_loc_Conversion::SetDstLoc(), SplitLocationForGap(), TruncateToCDS(), CAnnotMapping_Info::UpdateMappedSeq_loc(), UpgradeSeqLocId(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CContigItem::x_GatherInfo(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), x_GetSegSeqInfoViaCDS(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CSeq_loc_Mapper_Base::x_PushLocToDstMix(), x_PushRange(), CSeq_loc_Mapper_Base::x_PushSourceRange(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CGFFReader::x_ResolveLoc(), CVectorTrimPanel::x_SeqLocDelete(), CCDSTranslationPanel::x_SetLocationForProtein(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CGff3Writer::x_WriteFeatureContext(), and xgbloc_ver().

Definition at line 987 of file Seq_loc.hpp.

Referenced by CSeq_loc::Add(), CSeq_loc::Assign(), CSeq_loc::ChangeToMix(), CSeq_loc::CSeq_loc(), CSeq_loc::FlipStrand(), CSeq_loc::ResetStrand(), CSeq_loc::SetId(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeq_loc::SetStrand(), CSeq_loc::SetTruncatedStart(), CSeq_loc::SetTruncatedStop(), and CSeq_loc::x_ChangeToMix().

Override all setters to incorporate cache invalidation.

Definition at line 960 of file Seq_loc.hpp.

References CSeq_loc::InvalidateIdCache(), and CSeq_loc_Base::SetNull().

Referenced by CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CBedImportData::CBedImportData(), CFlatGapLoc::CFlatGapLoc(), CGtfImportData::CGtfImportData(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CSeq_loc_Conversion::ConvertEquiv(), CSeq_loc_Conversion_Set::ConvertEquiv(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CLocationEditPolicy::ConvertToOrder(), variation_ref::CVariationUtil::CreateFlankLocs(), variation::CVariationUtil::CreateFlankLocs(), CreateOrderedLoc(), CSeq_loc::CSeq_loc(), DealWithGenes(), CProteinAlignText::GetGenomicBounds(), CCreatedFeat_Ref::GetMappedLocation(), GetRandomSegment(), CLocationListCtrl::GetSeq_loc(), CBedImportData::Initialize(), CSeq_loc_CI_Impl::MakeLocOther(), CGff3LocationMerger::MergeLocation(), CGtfLocationMerger::MergeLocation(), CCompareSeqRegions::NextComparisonGroup(), CFastaReader::ReadOneSeq(), CXcompareAnnotsApplication::Run(), s_BlastSeqLoc2CSeqloc(), s_FlattenLoc(), s_LocationJoinToOrder(), s_NormalizeNullsBetween(), CNewCleanup_imp::SeqLocBC(), variation::CVariationUtil::x_AdjustDelinsToInterval(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), x_MergeAndSort(), x_MergeNoSort(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CXcompareAnnotsApplication::x_ProcessMappingRange(), CSeq_loc_Mapper_Base::x_PushNullLoc(), x_PushRange(), x_SingleRange(), x_SubAndSort(), x_SubNoSort(), XGapToSeqLocEx(), xgbgap(), and xgbloc_ver().

Definition at line 984 of file Seq_loc.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CWriteUtil::ChangeToPackedInt(), CCleanup::ClearInternalPartials(), CObjMgr_QueryFactory::CObjMgr_QueryFactory(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CorrectIntervalOrder(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateRowSeq_loc(), CSeqUtils::CreateSeq_loc(), CCleanup::ExtendStopPosition(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CScore_StartStopCodon::Get(), CSeqUtils::GetCdsMappingInfoFromRna(), CAddGlobalCodeBreak::GetCommand(), CProteinAlignText::GetGenomicBounds(), CRegexp_loc::GetLoc(), CAlnMultiWidget::GetMarks(), GetOverlappingFeatures(), CObjMgr_QueryFactory::GetTSeqLocVector(), CBedImportData::Initialize(), MakeDDFromSeqLoc(), CSeq_loc_CI_Impl::MakeLocPacked_int(), MakeSeqLocFromDD(), CSeqUtils::MixLocToLoc(), CSequenceIStreamBlastDB::next(), PackedSeqLocToMaskedQueryRegions(), PreserveTerminalCodons(), ProjectExon_newlogic(), ProjectExon_oldlogic(), ReverseComplementLocation(), s_BlastSeqLoc2CSeqloc(), s_ConvertToBlastQueries(), CSeq_loc_Conversion::s_ConvertToMix(), s_CreateBlastMask(), s_MakePackedInt(), s_MakePackedInt2(), s_SeqLocDelete(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CNewCleanup_imp::SeqLocBC(), CCleanup::SetCodeBreakLocation(), SplitLocationForGap(), CSingleCDSExceptionPanel::TransferDataFromWindow(), NTweakExon::TweakExon(), UpgradeSeqLocId(), CPhrap_Contig::x_AddReadLocFeats(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CNewCleanup_imp::x_BothStrandBC(), CFastaReader::x_CloseMask(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CWindowMaskerJob::x_CreateProjectItems(), CFeatGlyph::x_DrawProjectedRuler(), CFeatGlyph::x_DrawRuler(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeatureGenerator::SImplementation::x_MapFeature(), IEditingActionFeat::x_MergeFeatureLocation(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CVectorTrimPanel::x_SeqLocDelete(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CGff3Writer::xAssignFeature(), CFeatTableEdit::xGetGeneLocation(), and CGff3LocationMerger::xGetRecordLocation().

Definition at line 984 of file Seq_loc.hpp.

Referenced by CSeq_loc::Add(), CSeq_loc::Assign(), CSeq_loc::ChangeToPackedInt(), CSeq_loc::CSeq_loc(), CSeq_loc::FlipStrand(), CSeq_loc::ResetStrand(), CSeq_loc::SetId(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeq_loc::SetStrand(), CSeq_loc::SetTruncatedStart(), CSeq_loc::SetTruncatedStop(), and CSeq_loc::x_ChangeToPackedInt().

Definition at line 986 of file Seq_loc.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertPacked_pnt(), CorrectIntervalOrder(), CSeq_loc_CI_Impl::MakeLocPacked_pnt(), ReverseComplementLocation(), CSeq_loc_Conversion::s_ConvertToMix(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), SplitLocationForGap(), UpgradeSeqLocId(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), and CAutogeneratedCleanup::x_BasicCleanupSeqLoc().

Definition at line 986 of file Seq_loc.hpp.

Referenced by CSeq_loc::Add(), CSeq_loc::Assign(), CSeq_loc::CSeq_loc(), CSeq_loc::FlipStrand(), CSeq_loc::ResetStrand(), CSeq_loc::SetId(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeq_loc::SetStrand(), CSeq_loc::SetTruncatedStart(), CSeq_loc::SetTruncatedStop(), and CSeq_loc::x_ChangeToPackedPnt().

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

Definition at line 3280 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc::IsPartialStart(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CPacked_seqint::SetPartialStart(), CPacked_seqpnt::SetPartialStart(), CSeq_interval::SetPartialStart(), CSeq_loc_mix::SetPartialStart(), CSeq_point::SetPartialStart(), CSeq_loc::SetPnt(), val, and CSeq_loc_Base::Which().

Referenced by CExonFromCds::AddIntron(), CAutoDefFeatureClause::AddToLocation(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), AugmentPartialness(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CAutoDefParsedClause::CAutoDefParsedClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CFixForTransSplicing::CombineFeatures(), CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes(), CFeatureGenerator::ConvertLocToAnnot(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CreateFeatLocation(), CreateLoc(), CreateOrderedLoc(), CreateTwoIntLoc(), CExtendCDSToStop::ExtendmRNA(), ExtendToStopCodon(), FindNewLocations(), CCdsFromGeneMrnaExon::GetCommand(), CExonFromCds::GetCommand(), CExtendCDSToStop::GetCommand(), CFuseFeaturesDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CFeatureGenePanel::GetLocationForGene(), CBulkLocationPanel::GetLocForBioseq(), CCleanup::GetProteinLocationFromNucleotideLocation(), InheritPartialness(), ProjectExons(), RemapOtherProtFeats(), s_FinishLoc(), s_GetCdsSequence(), s_MapSingleAA(), SeqLocExtend(), CCleanup::SeqLocExtend(), SeqLocExtend3(), SeqLocExtend5(), SetPartial(), CFeatureGenerator::SImplementation::SetPartialFlags(), CSeq_loc_mix::SetPartialStart(), CFeatGapInfo::Split(), TransferPartialness(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), TruncateCDSAtStop(), TruncateSeqLoc(), CPromote::x_AddProtFeature(), CDisplaySeqalign::x_AddTranslationForLocalSeq(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CCorrectGenesDialog::x_CorrectPairInterval(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFindITSParser::x_CreateMiscRna(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CFindITSParser::x_CreateRRna(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CReportTrim::x_RetranslateCDS(), CCDSTranslationPanel::x_SetLocationForProtein(), CSeq_loc_Mapper_Base::x_StripExtraneousFuzz(), CFeatTrim::x_TrimLocation(), and CAdjustForConsensusSpliceSite::x_UpdateLocation().

Definition at line 3313 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc::IsPartialStop(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CPacked_seqint::SetPartialStop(), CPacked_seqpnt::SetPartialStop(), CSeq_interval::SetPartialStop(), CSeq_loc_mix::SetPartialStop(), CSeq_point::SetPartialStop(), CSeq_loc::SetPnt(), val, and CSeq_loc_Base::Which().

Referenced by CExonFromCds::AddIntron(), CAutoDefFeatureClause::AddToLocation(), CCDSTranslationPanel::AdjustForStopCodonHyperlinkClicked(), AdjustMappedStop(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), AugmentPartialness(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CAutoDefParsedClause::CAutoDefParsedClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CFixForTransSplicing::CombineFeatures(), CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes(), CFeatureGenerator::ConvertLocToAnnot(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CreateFeatLocation(), CreateLoc(), CreateOrderedLoc(), CreateTwoIntLoc(), ExtendCDSToStopCodon(), CExtendCDSToStop::ExtendmRNA(), CCleanup::ExtendStopPosition(), ExtendToStopCodon(), FindNewLocations(), CCdsFromGeneMrnaExon::GetCommand(), CExonFromCds::GetCommand(), CExtendCDSToStop::GetCommand(), CFuseFeaturesDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CFeatureGenePanel::GetLocationForGene(), CBulkLocationPanel::GetLocForBioseq(), CCleanup::GetProteinLocationFromNucleotideLocation(), InheritPartialness(), CCdsToMatPeptide::MergeConvert(), ProjectExons(), RemapOtherProtFeats(), s_FinishLoc(), s_GetCdsSequence(), s_MapSingleAA(), SeqLocExtend(), CCleanup::SeqLocExtend(), SeqLocExtend3(), SeqLocExtend5(), SetPartial(), CFeatureGenerator::SImplementation::SetPartialFlags(), CSeq_loc_mix::SetPartialStop(), CFeatGapInfo::Split(), TransferPartialness(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), TruncateCDSAtStop(), CTruncateCDS::TruncateProteinFeat(), TruncateSeqLoc(), CPromote::x_AddProtFeature(), CDisplaySeqalign::x_AddTranslationForLocalSeq(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CCorrectGenesDialog::x_CorrectPairInterval(), CFindITSParser::x_CreateMiscRna(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CFindITSParser::x_CreateRRna(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CReportTrim::x_RetranslateCDS(), CSeq_loc_Mapper_Base::x_SetLastTruncated(), CCDSTranslationPanel::x_SetLocationForProtein(), CSeq_loc_Mapper_Base::x_StripExtraneousFuzz(), CFeatTrim::x_TrimLocation(), and CAdjustForConsensusSpliceSite::x_UpdateLocation().

Definition at line 985 of file Seq_loc.hpp.

Referenced by CSeq_loc_mix::AddInterval(), BOOST_AUTO_TEST_CASE(), CVariationNormalizationDelIns::ConvertExpandedInsertionToDelIns(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPoint(), CreatePointLoc(), CBulkLocationPanel::GetLocForBioseq(), GetRandomSegment(), CSNPDbFeatIterator::GetSeq_feat(), GetSPSeqLoc(), MakeCLoc(), CSeq_loc_CI_Impl::MakeLocPoint(), MakePoint(), NormalizeLoc(), CStd_seg::OffsetRow(), CStd_seg::RemapToLoc(), SRelLoc::Resolve(), ReverseComplementLocation(), s_AddSitesToAnnot(), CSeq_loc_Conversion::s_ConvertToMix(), s_MakeMixLoc(), s_MakePointForLocationStop(), sConvertIntToPoint(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CNewCleanup_imp::SeqLocBC(), CSeq_loc_Conversion::SetDstLoc(), CSeqTableSetLocFuzzFromLim::SetInt(), CEditingActionFeatTranslExcept::SetValue(), SplitLocationForGap(), TruncateSeqLoc(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), UpgradeSeqLocId(), CFeatureTableReader_Imp::x_AddIntervalToFeature(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CNewCleanup_imp::x_BothStrandBC(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CLocationListCtrl::x_GetInterval(), CMacroFunction_ReplaceStopWithSelenocysteine::x_GetProteinLoc(), variation_ref::CHgvsParser::x_insertion(), variation_ref::CHgvsParser::x_InstToString(), variation_ref::CHgvsParser::x_location(), CReportEntry::x_MapPos(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation_ref::CHgvsParser::x_prot_pos(), x_PushRange(), CSeq_loc_Mapper_Base::x_RangeToSeq_loc(), CGFFReader::x_ResolveLoc(), CBioseq::x_SeqLoc_To_DeltaExt(), CFeaturePropagator::x_TruncateToStopCodon(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), and CGvfReader::xFeatureSetLocationPoint().

Definition at line 985 of file Seq_loc.hpp.

Referenced by CSeq_loc::Assign(), CSeq_loc::CSeq_loc(), CSeq_loc::FlipStrand(), CSeq_loc::ResetStrand(), CSeq_loc::SetId(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeq_loc::SetStrand(), CSeq_loc::SetTruncatedStart(), CSeq_loc::SetTruncatedStop(), and CSeq_loc::x_ChangeToPackedPnt().

Set iterator's position.

Definition at line 2642 of file Seq_loc.cpp.

References CSeq_loc_CI::GetSize(), CSeq_loc_CI::m_Index, NCBI_THROW_FMT, and CSeq_loc_CI::x_GetIteratorType().

Referenced by AdjustFeatureEnd3(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), BOOST_AUTO_TEST_CASE(), CSeq_loc_CI::CSeq_loc_CI(), CSeq_loc_I::CSeq_loc_I(), CLocationEditPolicy::Extend3(), CExtendCDSToStop::GetCommand(), CLocationEditPolicy::Is3AtEndOfSeq(), IsExtendable(), s_CheckAbutting(), SeqLocExtend3(), and CAdjustForConsensusSpliceSite::x_AdjustCDS3End().

Set the strand for all of the location's ranges.

Definition at line 5196 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CPacked_seqint::SetStrand(), CSeq_loc_mix::SetStrand(), CPacked_seqpnt_Base::SetStrand(), CSeq_interval_Base::SetStrand(), CSeq_point_Base::SetStrand(), and CSeq_loc_Base::Which().

Referenced by CExonFromCds::AddIntron(), BOOST_AUTO_TEST_CASE(), CMultiSeqInfo::CMultiSeqInfo(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CQueryFactoryInfo::CQueryFactoryInfo(), ExtendCDSToStopCodon(), ExtendLocationForTranslExcept(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), CProSplign::FindGlobalAlignment(), CGeneFinder::GeneSearchNormalizeLoc(), CExonFromCds::GetCommand(), CExtendCDSToStop::GetCommand(), CGeneFinder::GetFeatViaSubsetThenExtremesIfPossible(), CProteinAlignText::GetGenomicBounds(), GetOverlappingFeatures(), IsGeneLocationOk(), CCleanup::ParseCodeBreak(), RemapAlignToLoc(), s_CollectBestOverlaps(), s_ConvertToBlastQueries(), s_ParseTRnaFromAnticodonString(), CGeneFinder::CGeneSearchPlugin::setUpFeatureIterator(), variation_ref::CVariationUtil::SetVariantProperties(), TestMapper_Trimming(), TruncateSeqLoc(), TryOneCaseMixLoc(), CBlastDB_FastaFormatter::Write(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CCorrectGenesDialog::x_CorrectPairInterval(), CCorrectGenesDialog::x_CorrectPairStrand(), CProSplignJob::x_CreateProjectItems(), CFeaturePropagator::x_ExtendToStopCodon(), x_GetBestOverlapForSNP(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_PushSourceRange(), CSplitQueryTestFixture::x_ReadQueryBoundsPerChunk(), CCDSTranslationPanel::x_SetLocationForProtein(), CFeaturePropagator::x_TruncateToStopCodon(), and CGvfReader::xFeatureSetLocationPoint().

Set the range to position.

Definition at line 2829 of file Seq_loc.cpp.

References info, CSeq_loc_CI::m_Impl, CSeq_loc_CI_Impl::UpdateLoc(), CSeq_loc_CI::x_CheckValid(), and CSeq_loc_I::x_GetRangeInfo().

Referenced by CEditSequence::AdjustFeatureLocations(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds(), CEditSequence::AdjustProtFeatureLocations(), CFuseJoinsInLocs::apply(), BOOST_AUTO_TEST_CASE(), CSequenceUpdater::s_OffsetLocation(), CAlignmentAssistant::TranslateLocations(), CFeatGlyph::x_AdjustFrame(), and CFeaturePropagator::x_MapLocation().

set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc)

Definition at line 3398 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc::IsTruncatedStart(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CPacked_seqint::SetTruncatedStart(), CPacked_seqpnt::SetTruncatedStart(), CSeq_interval::SetTruncatedStart(), CSeq_loc_mix::SetTruncatedStart(), CSeq_point::SetTruncatedStart(), val, and CSeq_loc_Base::Which().

Referenced by InheritPartialness(), CSeq_loc_mix::SetTruncatedStart(), and TransferPartialness().

Definition at line 3431 of file Seq_loc.cpp.

References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc::IsTruncatedStop(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CPacked_seqint::SetTruncatedStop(), CPacked_seqpnt::SetTruncatedStop(), CSeq_interval::SetTruncatedStop(), CSeq_loc_mix::SetTruncatedStop(), CSeq_point::SetTruncatedStop(), val, and CSeq_loc_Base::Which().

Referenced by InheritPartialness(), CSeq_loc_mix::SetTruncatedStop(), TransferPartialness(), and CSeq_loc_Mapper_Base::x_SetLastTruncated().

Definition at line 982 of file Seq_loc.hpp.

Referenced by AddSpanningSentinelFeat(), CSourceModParser::ApplyAllMods(), BOOST_AUTO_TEST_CASE(), BuildGoodSegSet(), CComponentSearchForm::ConstructQuery(), CCpgSearchForm::ConstructQuery(), CFeatureSearchForm::ConstructQuery(), COrfSearchForm::ConstructQuery(), Convert_Seq_annot_Seq_loc_All(), Convert_Seq_entry_Seq_loc(), Convert_Seq_feat_Seq_loc_dbxref_Loc(), Convert_Seq_id_Seq_loc(), CPSeq::CPSeq(), variation::CreateUnknownProtConsequenceVariation(), CreateWholeSeqLocFromIds(), CTestObjMgr::CreateWholeSSeqLoc(), CReferenceItem::CReferenceItem(), CRemoveFeatChecker::Do(), CFlatFileGenerator::Generate(), CScore_StartStopCodon::Get(), CFindRSites::GetAnnot(), CProjectTreeView::GetMultiple(), CBioseq_Handle::GetRangeSeq_loc(), CProjectTreeView::GetSearchLoc(), CViewGraphic::GetSearchLoc(), GetSeqExt(), CFlatFileLocusItem::GetSeqLoc(), CVDBSeqInfoSrc::GetSeqLoc(), GetSeqLocFromStream(), CBlastKmerResults::GetTSL(), CwxDemoAlignTableFrame::InitData(), IsInScope(), CwxDemoFeatureTableFrame::LoadAccession(), CwxDemoFeatureTableFrame::LoadFile(), CTblastnNode::Main(), CMakeCdrProds::MakeCdrProds(), CSeq_loc_CI_Impl::MakeLocOther(), CAliToSeq_align::MakeSeq_align(), CIdMapper::Map(), CGencollIdMapperAdapter::Map(), CGencollIdMapperAdapter::MapObject(), ReadFastaQueries(), CSeqUtils::RemapChildToParent(), CAnnotationASN1::CImplementationData::ResetASN1(), CPsiBlastApp::Run(), CSeedTop::Run(), CVectorScreen::Run(), CLocalFinderApp::Run(), CXcompareAnnotsApplication::Run(), CVDBTblastnApp::Run(), CDemoApp::Run(), CTestBMApp::Run(), VSRunSampleApplication::Run(), CSampleLds2Application::Run(), CFeatTreeSampleApp::Run(), CSampleObjmgrApplication::Run(), CTestTranscript_CountCdregions::RunTest(), s_AddPartToSegmentedBioseq(), s_ConvertToBlastQueries(), s_CreateSeqLocMapper(), s_GCSeqsToSeqLocs(), s_GetProteinName(), s_GetUngapLoc(), s_RemapChildToParent(), s_Seq_align_Seq_loc(), CPsiBlastTestFixture::s_SetupSubject(), s_SetupWithMultipleQueriesAndSubjects(), BlastEngineTestFixture::setupQueryAndSubject(), setupQueryInfoForOffsetTranslation(), CSeqTableLocColumns::UpdateSeq_loc(), UpgradeSeqLocId(), CFastaOstream::Write(), CFastaOstreamComp::Write(), CPromote::x_AddProtFeature(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CBlastSampleApplication::x_CreateSSeqLoc(), CFeatGlyph::x_DrawRuler(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CSplignApp::x_GetBl2SeqHits(), CReportEntry::x_GetCCoordinate(), CAsn2FlatApp::x_GetLocation(), CFlatFileGenerator::x_GetLocation(), CDeflineGenerator::x_GetLongestProtein(), x_GetSeqLocFromStream(), CFastaExportJob::x_GetWholeLoc(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CSplitQueryTestFixture::x_PrepareBlastQueryStructures(), x_PushRange(), CSeq_loc_Mapper_Base::x_PushSourceRange(), CBlastFormatterApp::x_QueryBioseqToSSeqLoc(), CBlastFormatterVdbApp::x_QueryBioseqToSSeqLoc(), CSeq_loc_Mapper_Base::x_RangeToSeq_loc(), CTblastnApp::x_RunMTBySplitDB(), CBLASTToolManager::x_SelectCompatibleInputObjects(), CBioseqContext::x_SetLocation(), CReportEntry::x_SetMrnaMapper(), CPsiBl2SeqTestFixture::x_SetupSubject(), CSeqTest::x_TestAllCdregions(), CVectorTrimPanel::x_TrimSelected(), CGff3Writer::x_WriteFeatureContext(), CGff3Writer::x_WriteSeqAnnotHandle(), and xgbloc_ver().

Definition at line 1042 of file Seq_loc.cpp.

Subtract seq-loc from this, merge/sort resulting ranges depending on flags.

Return a new seq-loc object.

Definition at line 5087 of file Seq_loc.cpp.

References flags, CSeq_loc::fMerge_SingleRange, CSeq_loc::fSort, CSeq_loc::fStrand_Ignore, ISynonymMapper::GetBestSynonym(), IsReverse(), x_SingleRange(), x_SubAndSort(), and x_SubNoSort().

Referenced by variation_ref::CVariationUtil::AdjustDelinsToInterval(), BOOST_AUTO_TEST_CASE(), fta_seqloc_del_far(), CSeq_loc::Intersect(), Seq_loc_Subtract(), CFeatureItem::x_AddQualsProt(), variation::CVariationUtil::x_AdjustDelinsToInterval(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), and CFeatTrim::x_TrimLocation().

Definition at line 429 of file Seq_loc.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, CPacked_seqint_Base::Get(), CSeq_loc_equiv_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_bond_Base::GetA(), CSeq_bond_Base::GetB(), CSeq_loc_Base::GetBond(), COpenRange< TSeqPos >::GetEmpty(), CSeq_loc_Base::GetEmpty(), CSeq_loc_Base::GetEquiv(), CSeq_interval_Base::GetFrom(), CPacked_seqpnt_Base::GetId(), CSeq_interval_Base::GetId(), CSeq_point_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CPacked_seqpnt_Base::GetPoints(), CSeq_interval_Base::GetTo(), COpenRange< TSeqPos >::GetWhole(), CSeq_loc_Base::GetWhole(), CSeq_bond_Base::IsSetB(), ITERATE, NCBI_THROW_FMT, pi, CSeq_loc_Base::SelectionName(), COpenRange< Position >::Set(), CSeq_loc_Base::Which(), and CSeq_loc::x_UpdateId().

Referenced by CSeq_loc::x_UpdateTotalRange().

Definition at line 3772 of file Seq_loc.cpp.

References _ASSERT, CPacked_seqpnt::AddPoint(), CPacked_seqpnt::AddPoints(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CPacked_seqpnt_Base::GetPoints(), CSeq_point_Base::GetStrand(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), CSeq_point_Base::IsSetFuzz(), CSeq_point_Base::IsSetId(), CSeq_point_Base::IsSetStrand(), CPacked_seqpnt_Base::SetFuzz(), CSeq_point_Base::SetFuzz(), CPacked_seqpnt_Base::SetId(), CSeq_point_Base::SetId(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CPacked_seqpnt_Base::SetStrand().

Referenced by CSeq_loc::Add().

Definition at line 3541 of file Seq_loc.cpp.

References CSeq_bond_Base::CanGetA(), CSeq_bond_Base::CanGetB(), 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, Get(), CPacked_seqint_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_bond_Base::GetA(), CSeq_bond_Base::GetB(), CSeq_loc_Base::GetBond(), CSeq_loc_Base::GetEmpty(), CSeq_loc_Base::GetEquiv(), CPacked_seqpnt_Base::GetId(), CSeq_interval_Base::GetId(), CSeq_point_Base::GetId(), 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(), ITERATE, NCBI_THROW_FMT, CSeq_loc_Base::SelectionName(), CSeq_loc_Base::Which(), and CSeq_loc::x_UpdateId().

Referenced by CSeq_loc::CheckId().

Definition at line 1013 of file Seq_loc.hpp.

References CSeq_loc_CI::x_IsValid(), and CSeq_loc_CI::x_ThrowNotValid().

Referenced by CSeq_loc_I::Delete(), CSeq_loc_CI::GetBondRange(), CSeq_loc_CI::GetEmbeddingSeq_loc(), CSeq_loc_CI::GetEquivPartRange(), CSeq_loc_I::GetEquivPartRange(), CSeq_loc_CI::GetEquivSetRange(), CSeq_loc_I::GetEquivSetRange(), CSeq_loc_CI::GetEquivSetsCount(), CSeq_loc_CI::GetFuzzFrom(), CSeq_loc_CI::GetFuzzTo(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSeq_id_Handle(), CSeq_loc_CI::GetStrand(), CSeq_loc_CI::IsBondA(), CSeq_loc_CI::IsBondB(), CSeq_loc_CI::IsEmpty(), CSeq_loc_CI::IsInBond(), CSeq_loc_CI::IsInEquivSet(), CSeq_loc_CI::IsPoint(), CSeq_loc_CI::IsSetStrand(), CSeq_loc_CI::IsWhole(), CSeq_loc_I::MakeBondA(), CSeq_loc_I::MakeBondAB(), CSeq_loc_I::MakeBondB(), CSeq_loc_CI::operator++(), CSeq_loc_I::RemoveBond(), CSeq_loc_I::ResetFuzz(), CSeq_loc_I::ResetFuzzFrom(), CSeq_loc_I::ResetFuzzTo(), CSeq_loc_I::ResetStrand(), CSeq_loc_I::SetFrom(), CSeq_loc_I::SetFuzz(), CSeq_loc_I::SetFuzzFrom(), CSeq_loc_I::SetFuzzTo(), CSeq_loc_I::SetPoint(), CSeq_loc_I::SetRange(), CSeq_loc_I::SetSeq_id_Handle(), CSeq_loc_I::SetStrand(), and CSeq_loc_I::SetTo().

Definition at line 2691 of file Seq_loc.cpp.

References CSeq_loc_CI_Impl::GetRanges(), CSeq_loc_CI::m_Impl, and CSeq_loc_CI::m_Index.

Referenced by CSeq_loc_I::ResetFuzz(), CSeq_loc_I::ResetFuzzFrom(), CSeq_loc_I::ResetFuzzTo(), CSeq_loc_I::ResetStrand(), CSeq_loc_I::SetFrom(), CSeq_loc_I::SetFuzz(), CSeq_loc_I::SetFuzzFrom(), CSeq_loc_I::SetFuzzTo(), CSeq_loc_I::SetPoint(), CSeq_loc_I::SetRange(), CSeq_loc_I::SetSeq_id_Handle(), CSeq_loc_I::SetStrand(), and CSeq_loc_I::SetTo().

Definition at line 2629 of file Seq_loc.cpp.

References CSeq_loc_CI_Impl::GetRanges(), CSeq_loc_CI::m_Impl, and CSeq_loc_CI::m_Index.

Referenced by CSeq_loc_CI::GetEmbeddingSeq_loc(), CSeq_loc_CI::GetFuzzFrom(), CSeq_loc_CI::GetFuzzTo(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSeq_id_Handle(), CSeq_loc_CI::GetStrand(), CSeq_loc_CI::IsEmpty(), CSeq_loc_CI::IsPoint(), CSeq_loc_CI::IsSetStrand(), and CSeq_loc_CI::IsWhole().

Definition at line 186 of file Seq_loc.cpp.

Definition at line 423 of file Seq_loc.hpp.

Definition at line 263 of file Seq_loc.hpp.

Definition at line 411 of file Seq_loc.hpp.

Definition at line 1049 of file Seq_loc.cpp.

Definition at line 577 of file Seq_loc.hpp.

Referenced by CSeq_loc_I::Delete(), CSeq_loc_CI::GetBondRange(), CSeq_loc_I::GetEquivMode(), CSeq_loc_CI::GetEquivPartRange(), CSeq_loc_I::GetEquivPartRange(), CSeq_loc_CI::GetEquivSetRange(), CSeq_loc_I::GetEquivSetRange(), CSeq_loc_CI::GetEquivSetsCount(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::GetSize(), CSeq_loc_I::HasChanges(), CSeq_loc_CI::HasEquivSets(), CSeq_loc_I::InsertEmpty(), CSeq_loc_I::InsertInterval(), CSeq_loc_I::InsertNull(), CSeq_loc_I::InsertPoint(), CSeq_loc_I::InsertWhole(), CSeq_loc_CI::IsBondA(), CSeq_loc_CI::IsBondB(), CSeq_loc_CI::IsInBond(), CSeq_loc_CI::IsInEquivSet(), CSeq_loc_I::MakeBondA(), CSeq_loc_I::MakeBondAB(), CSeq_loc_I::MakeBondB(), CSeq_loc_I::MakeSeq_loc(), CSeq_loc_CI::operator=(), CSeq_loc_CI::operator==(), CSeq_loc_I::RemoveBond(), CSeq_loc_I::ResetFuzz(), CSeq_loc_I::ResetFuzzFrom(), CSeq_loc_I::ResetFuzzTo(), CSeq_loc_I::ResetStrand(), CSeq_loc_I::SetEquivMode(), CSeq_loc_I::SetFrom(), CSeq_loc_I::SetFuzz(), CSeq_loc_I::SetFuzzFrom(), CSeq_loc_I::SetFuzzTo(), CSeq_loc_I::SetPoint(), CSeq_loc_I::SetRange(), CSeq_loc_I::SetSeq_id_Handle(), CSeq_loc_I::SetStrand(), CSeq_loc_I::SetTo(), CSeq_loc_I::x_GetRangeInfo(), CSeq_loc_CI::x_GetRangeInfo(), CSeq_loc_CI::x_IsValid(), and CSeq_loc_I::x_IsValidForInsert().

Definition at line 586 of file Seq_loc.hpp.

Referenced by CSeq_loc_I::Delete(), CSeq_loc_CI::GetBondRange(), CSeq_loc_CI::GetEquivPartRange(), CSeq_loc_I::GetEquivPartRange(), CSeq_loc_CI::GetEquivSetRange(), CSeq_loc_I::GetEquivSetRange(), CSeq_loc_CI::GetEquivSetsCount(), CSeq_loc_CI::GetPos(), CSeq_loc_I::InsertEmpty(), CSeq_loc_I::InsertInterval(), CSeq_loc_I::InsertNull(), CSeq_loc_I::InsertPoint(), CSeq_loc_I::InsertWhole(), CSeq_loc_CI::IsBondA(), CSeq_loc_CI::IsBondB(), CSeq_loc_CI::IsInBond(), CSeq_loc_CI::IsInEquivSet(), CSeq_loc_I::MakeBondA(), CSeq_loc_I::MakeBondAB(), CSeq_loc_I::MakeBondB(), CSeq_loc_CI::operator++(), CSeq_loc_CI::operator=(), CSeq_loc_CI::operator==(), CSeq_loc_I::RemoveBond(), CSeq_loc_CI::Rewind(), CSeq_loc_CI::SetPos(), CSeq_loc_I::x_GetRangeInfo(), CSeq_loc_CI::x_GetRangeInfo(), CSeq_loc_CI::x_IsValid(), and CSeq_loc_I::x_IsValidForInsert().

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