Na_strand.hpp File Reference

#include <objects/seqloc/Na_strand_.hpp>

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Enumerations
enum	EIsSetStrand { eIsSetStrand_Any , eIsSetStrand_All }
	Flag used by IsSetStrand() to switch between any/all modes. More...
enum	ESeqLocExtremes { eExtreme_Biological , eExtreme_Positional }
	Used to determine the meaning of a location's Start/Stop positions. More...

Functions
bool	IsForward (ENa_strand s)
bool	IsReverse (ENa_strand s)
bool	SameOrientation (ENa_strand a, ENa_strand b)
ENa_strand	Reverse (ENa_strand s)

Enumeration Type Documentation

EIsSetStrand

enum EIsSetStrand

Flag used by IsSetStrand() to switch between any/all modes.

Enumerator
eIsSetStrand_Any	Check if any part has strand.
eIsSetStrand_All	Check if all parts have strand.

Definition at line 51 of file Na_strand.hpp.

ESeqLocExtremes

enum ESeqLocExtremes

Used to determine the meaning of a location's Start/Stop positions.

On the minus strand the numerical values are different than the biological ones.

See also

CSeq_loc::GetStart(), CSeq_loc::GetStop()

Enumerator
eExtreme_Biological	5' and 3'
eExtreme_Positional	numerical value

Definition at line 61 of file Na_strand.hpp.

Function Documentation

IsForward()

bool IsForward ( ENa_strand  s )

inline

Definition at line 68 of file Na_strand.hpp.

References eNa_strand_both, and eNa_strand_plus.

Referenced by CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), IBlastSeqVector::GetStrandData(), CNSeq::Init(), CAliToSeq_align::NucPosOut(), CMapControl::OnKeyDown(), CRichTextCtrl::OnKeyDown(), CAliToSeq_align::SetExonBioEnd(), CAliToSeq_align::SetExonBioStart(), CSeqTableLocColumns::SetTableKeyAndIndex(), and CSeq_align_Mapper_Base::x_GetDstSparse().

IsReverse()

bool IsReverse ( ENa_strand  s )

inline

Definition at line 75 of file Na_strand.hpp.

References eNa_strand_both_rev, and eNa_strand_minus.

Referenced by CHandleRangeMap::AddRange(), CDefaultSpotIdDetector::AddSpotId(), BOOST_AUTO_TEST_CASE(), CMappingRange::CanMap(), CAnnotCompare::CompareFeats(), CSeq_feat::CompareNonLocation(), CSeq_loc::CompareSubLoc(), ConvertDendiagToPairwiseAln(), ConvertDensegToPairwiseAln(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertPackedsegToPairwiseAln(), ConvertSeqLocsToPairwiseAln(), CSeq_loc_Conversion::ConvertSimpleMix(), ConvertSparseToPairwiseAln(), ConvertSplicedToPairwiseAln(), CSeq_align::CreateDensegFromDisc(), CDense_seg::CreateRowSeq_interval(), CHandleRange::GetCircularRangeEnd(), CHandleRange::GetCircularRangeStart(), CHandleRange::GetLeft(), GetOverlappingFeatures(), CHandleRange::GetOverlappingRange(), CProductStringBuilder::GetProductString(), CHandleRange::GetRight(), CSeqMap::GetSeqMapForSeq_loc(), CSeqVector_CI::HasZeroGapBefore(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), CPacked_seqint::IsReverseStrand(), CSeq_loc::IsReverseStrand(), CSeq_loc_mix::IsReverseStrand(), LocationOffset(), CAnnotObjectType_Less::operator()(), SCigarAlignment::operator()(), ProductToSource(), SRelLoc::Resolve(), s_AddSitesToAnnot(), s_CalculateStarts(), s_CheckAbutting(), s_GetCIGARForSort(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetNeighborhoodLocs(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetStartAndStopCodonsLocs(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetUTRLocs(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangeInfoMap(), s_SeqLocToTotalRangesInfoMapByStrand(), SameOrientation(), SSeqMapSelector::SetStrand(), CSeqVector_CI::SetStrand(), CSeqTableLocColumns::SetTableKeyAndIndex(), SourceToProduct(), SRelLoc::SRelLoc(), CSeq_loc::Subtract(), CAlignmentAssistant::TranslateLocations(), CFlatSeqLoc::x_Add(), CSeq_loc_Mapper_Base::x_AddExonPartsMapping(), CRangeWithFuzz::x_AddFuzz(), CSeqMap::x_AddSegment(), CCompareSeq_locs::x_Compare(), CSeq_align_Mapper_Base::x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), x_FindRSite(), CSeq_align_Mapper_Base::x_GetDstExon(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeq_align_Mapper_Base::x_GetDstStd(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CSeq_loc_Mapper_Base::x_GetRangeLength(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CSeq_interval::x_IsMinusStrand(), CSeq_loc_Mapper_Base::x_IterateExonParts(), CSeq_loc_Mapper_Base::x_MapInterval(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapNextRange(), x_MatchStrand(), x_MergeAndSort(), x_MergeRanges(), CSeq_loc_Mapper_Base::x_NextMappingRange(), CSeq_loc_Mapper_Base::x_PushMappedRange(), CSeq_align_Mapper_Base::x_PushSeg(), x_RangesToSeq_loc(), CGFFReader::x_ResolveLoc(), CSeq_loc_Mapper_Base::x_ReverseRangeOrder(), CAnnot_Collector::x_SearchRange(), CBioseqContext::x_SetLocation(), x_SingleRange(), x_SubAndSort(), x_SubNoSort(), and x_TestGetFilteredQueryRegions().

Reverse()

ENa_strand Reverse ( ENa_strand  s )

inline

Definition at line 90 of file Na_strand.hpp.

References eNa_strand_both, eNa_strand_both_rev, eNa_strand_minus, eNa_strand_plus, and eNa_strand_unknown.

Referenced by CHandleRangeMap::AddRange(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion::ConvertPoint(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_loc_Conversion::ConvertStrand(), CPacked_seqpnt::FlipStrand(), CSeq_interval::FlipStrand(), CSeq_point::FlipStrand(), GetReverseComplement(), CSeq_loc_Conversion::MakeDstMix(), CMappingRange::Map_Strand(), CNewCleanup_imp::PCRReactionSetBC(), SRelLoc::Resolve(), s_AddSitesToAnnot(), s_SeqIntRevCmp(), s_SeqPntRevCmp(), SRelLoc::SRelLoc(), CAlignmentAssistant::TranslateLocations(), CAnnot_Collector::x_CollectMapped(), x_FindRSite(), CSeq_align_Mapper_Base::x_GetDstSparse(), CNewCleanup_imp::x_ModernizePCRPrimers(), CAnnot_Collector::x_SearchMapped(), and CFastaOstream::x_WriteSequence().

SameOrientation()

bool SameOrientation ( ENa_strand  a, ENa_strand  b  )

inline

Definition at line 83 of file Na_strand.hpp.

References a, b, and IsReverse().

Referenced by CAnnotCompare::CompareFeats(), IsConsistent(), SAlignment_Segment::SAlignment_Row::SameStrand(), SRelLoc::SRelLoc(), variation::CVariationUtil::TranslateNAtoAA(), CSequenceUpdater::Update(), CSeq_loc_Mapper_Base::x_AddConversion(), CCompareSeq_locs::x_Compare(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CSeq_align_Mapper_Base::x_HaveMixedStrand(), and CSeq_loc_Mapper_Base::x_PushSourceRange().