loc_edit.hpp File Reference

#include <corelib/ncbistd.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqfeat/Seq_feat.hpp>

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Classes
class	CLocationEditPolicy

Enumerations
enum	ESplitLocOptions { eSplitLocOption_make_partial = 0x01 , eSplitLocOption_split_in_exon = 0x02 , eSplitLocOption_split_in_intron = 0x04 }

Functions
string	PrintBestSeqId (const CSeq_id &sid, CScope &scope)
string	PrintSeqIntUseBestID (const CSeq_interval &seq_int, CScope &scope, bool range_only)
string	PrintPntAndPntsUseBestID (const CSeq_loc &seq_loc, CScope &scope, bool range_only=false)
string	SeqLocPrintUseBestID (const CSeq_loc &seq_loc, CScope &scope, bool range_only=false)
bool	ApplyPolicyToFeature (const CLocationEditPolicy &policy, const CSeq_feat &orig_feat, CScope &scope, bool adjust_gene, bool retranslate_cds)
CRef< CSeq_loc >	SeqLocExtend (const CSeq_loc &loc, size_t pos, CScope *scope)
void	ReverseComplementLocation (CSeq_loc &loc, CScope &scope)
void	ReverseComplementFeature (CSeq_feat &feat, CScope &scope)
void	SeqLocAdjustForTrim (CSeq_loc &loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted)
void	SeqLocAdjustForInsert (CSeq_loc &loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid)
void	FeatureAdjustForTrim (CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, bool &bAdjusted)
void	FeatureAdjustForInsert (CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid)
void	SplitLocationForGap (CSeq_loc &loc1, CSeq_loc &loc2, size_t start, size_t stop, const CSeq_id *seqid, unsigned int options=eSplitLocOption_make_partial|eSplitLocOption_split_in_exon)
bool	CorrectIntervalOrder (CSeq_loc &loc)
	Correct the order of consecutive intervals with the same Seq-id on the same strand. More...
bool	ExtendPartialFeatureEnds (CBioseq_Handle bsh)
bool	IsExtendable (const CSeq_feat &cds, CScope &scope)

Enumeration Type Documentation

ESplitLocOptions

enum ESplitLocOptions

Enumerator
eSplitLocOption_make_partial
eSplitLocOption_split_in_exon
eSplitLocOption_split_in_intron

Definition at line 160 of file loc_edit.hpp.

Function Documentation

ApplyPolicyToFeature()

bool ApplyPolicyToFeature	(	const CLocationEditPolicy &	policy,
		const CSeq_feat &	orig_feat,
		CScope &	scope,
		bool	adjust_gene,
		bool	retranslate_cds
	)

Definition at line 835 of file loc_edit.cpp.

References AdjustForCDSPartials(), CLocationEditPolicy::ApplyPolicyToFeature(), CSerialObject::Assign(), eExtreme_Biological, CSeq_feat_Handle::GetAnnot(), CSeq_feat_Base::GetData(), CSeq_entry_Handle::GetEditHandle(), CSeq_feat_Base::GetLocation(), GetOverlappingGene(), CSeq_annot_Handle::GetParentEntry(), CScope::GetSeq_featHandle(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetProduct(), l(), CSeq_feat_EditHandle::Replace(), RetranslateCDS(), SeqLocExtend3(), SeqLocExtend5(), and CSeq_feat_Base::SetLocation().

Referenced by BOOST_AUTO_TEST_CASE().

CorrectIntervalOrder()

bool CorrectIntervalOrder

(

CSeq_loc &

loc

)

Correct the order of consecutive intervals with the same Seq-id on the same strand.

Definition at line 2346 of file loc_edit.cpp.

References CorrectIntervalOrder(), 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::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), and CSeq_loc_Base::Which().

Referenced by CCorrectIntervalOrder::ApplyToCSeq_entry(), and BOOST_AUTO_TEST_CASE().

ExtendPartialFeatureEnds()

bool ExtendPartialFeatureEnds

(

CBioseq_Handle

bsh

)

Definition at line 2585 of file loc_edit.cpp.

References AdjustFeatureEnd3(), AdjustFeatureEnd5(), CSerialObject::Assign(), CSeqFeatData::eSubtype_mRNA, f, CSeq_feat_Handle::GetOriginalSeq_feat(), CBioseq_Handle::GetScope(), CSeq_feat_EditHandle::Replace(), and RetranslateCDS().

Referenced by CheckAdjustStart(), CheckAdjustStartAndStop(), CheckAdjustStop(), and CTable2AsnValidator::Cleanup().

FeatureAdjustForInsert()

void FeatureAdjustForInsert	(	CSeq_feat &	feat,
		TSeqPos	from,
		TSeqPos	to,
		const CSeq_id *	seqid
	)

Definition at line 2141 of file loc_edit.cpp.

References CdregionAdjustForInsert(), CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_tRNA, CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetData(), SeqLocAdjustForInsert(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and TrnaAdjustForInsert().

Referenced by ConvertRawToDeltaByNs().

FeatureAdjustForTrim()

void FeatureAdjustForTrim	(	CSeq_feat &	feat,
		TSeqPos	from,
		TSeqPos	to,
		const CSeq_id *	seqid,
		bool &	bCompleteCut,
		bool &	bAdjusted
	)

Definition at line 2087 of file loc_edit.cpp.

References CdregionAdjustForTrim(), CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_tRNA, CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetData(), SeqLocAdjustForTrim(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and TrnaAdjustForTrim().

Referenced by ConvertRawToDeltaByNs().

IsExtendable()

bool IsExtendable	(	const CSeq_feat &	cds,
		CScope &	scope
	)

Definition at line 2555 of file loc_edit.cpp.

References eExtreme_Positional, CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CRange_Base::GetFrom(), CSeq_feat_Base::GetLocation(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSize(), CSeq_loc::GetStop(), IsExtendableLeft(), IsExtendableRight(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), and CSeq_loc_CI::SetPos().

Referenced by CheckAdjustStart(), CheckAdjustStartAndStop(), and CheckAdjustStop().

PrintBestSeqId()

string PrintBestSeqId	(	const CSeq_id &	sid,
		CScope &	scope
	)

Definition at line 64 of file loc_edit.cpp.

References CSeq_id::AsFastaString(), eGetId_Best, GetId(), CSeq_id_Handle::GetSeqId(), and kEmptyStr.

Referenced by PrintPntAndPntsUseBestID(), and PrintSeqIntUseBestID().

PrintPntAndPntsUseBestID()

string PrintPntAndPntsUseBestID	(	const CSeq_loc &	seq_loc,
		CScope &	scope,
		bool	range_only = false
	)

Definition at line 131 of file loc_edit.cpp.

References CPacked_seqpnt_Base::GetId(), CSeq_point_Base::GetId(), CSeq_loc::GetLabel(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), kEmptyStr, location, PrintBestSeqId(), and strtmp.

Referenced by SeqLocPrintUseBestID().

PrintSeqIntUseBestID()

string PrintSeqIntUseBestID	(	const CSeq_interval &	seq_int,
		CScope &	scope,
		bool	range_only
	)

Definition at line 82 of file loc_edit.cpp.

References CSeq_interval_Base::CanGetFuzz_from(), CSeq_interval_Base::CanGetFuzz_to(), CSeq_interval_Base::CanGetStrand(), eNa_strand_both_rev, eNa_strand_minus, eNa_strand_unknown, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CInt_fuzz::GetLabel(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), int, NStr::IntToString(), kEmptyStr, location, PrintBestSeqId(), and strand_symbol.

Referenced by SeqLocPrintUseBestID().

ReverseComplementFeature()

void ReverseComplementFeature	(	CSeq_feat &	feat,
		CScope &	scope
	)

Definition at line 1068 of file loc_edit.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_tRNA, CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), ReverseComplementCDRegion(), ReverseComplementLocation(), ReverseComplementTrna(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CMixedStrands::GetCommand(), GetReverseComplimentSequenceCommand(), and CRevCompSequencesDlg::RevCompBioSeq().

ReverseComplementLocation()

void ReverseComplementLocation	(	CSeq_loc &	loc,
		CScope &	scope
	)

Definition at line 991 of file loc_edit.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::InvalidateCache(), CSeq_bond_Base::IsSetA(), CSeq_bond_Base::IsSetB(), NON_CONST_ITERATE, ReverseComplementLocation(), CSeq_loc::SetBond(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), and CRevCompSequencesDlg::RevCompBioSeq().

SeqLocAdjustForInsert()

void SeqLocAdjustForInsert	(	CSeq_loc &	loc,
		TSeqPos	from,
		TSeqPos	to,
		const CSeq_id *	seqid
	)

Definition at line 1682 of file loc_edit.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, SeqLocAdjustForInsert(), CSeq_loc::SetBond(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE().

SeqLocAdjustForTrim()

void SeqLocAdjustForTrim	(	CSeq_loc &	loc,
		TSeqPos	from,
		TSeqPos	to,
		const CSeq_id *	seqid,
		bool &	bCompleteCut,
		TSeqPos &	trim5,
		bool &	bAdjusted
	)

Definition at line 1489 of file loc_edit.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, NormalizeLoc(), SeqLocAdjustForTrim(), CSeq_loc::SetBond(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().

Referenced by CFeatGapInfo::AdjustProteinSeq(), and BOOST_AUTO_TEST_CASE().

SeqLocExtend()

CRef<CSeq_loc> SeqLocExtend	(	const CSeq_loc &	loc,
		size_t	pos,
		CScope *	scope
	)

Definition at line 546 of file loc_edit.cpp.

References eExtreme_Positional, CSeq_loc::fMerge_AbuttingOnly, CSeq_loc::fSort, CSeq_loc::GetId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), Seq_loc_Add(), CSeq_loc::SetPartialStart(), and CSeq_loc::SetPartialStop().

Referenced by AdjustGene(), CEditSequenceEnds::Extend3(), CEditSequenceEnds::Extend5(), and ExtendCDSToStopCodon().

SeqLocPrintUseBestID()

string SeqLocPrintUseBestID	(	const CSeq_loc &	seq_loc,
		CScope &	scope,
		bool	range_only = false
	)

Definition at line 153 of file loc_edit.cpp.

References CSeq_bond_Base::CanGetB(), 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(), CSeq_loc_Base::GetEquiv(), CSeq_loc_Base::GetInt(), CSeq_loc::GetLabel(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::IsBond(), CSeq_loc_Base::IsEquiv(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), ITERATE, kEmptyStr, location, PrintPntAndPntsUseBestID(), PrintSeqIntUseBestID(), and CSeq_loc::SetBond().

Referenced by BOOST_AUTO_TEST_CASE().

SplitLocationForGap()

void SplitLocationForGap	(	CSeq_loc &	loc1,
		CSeq_loc &	loc2,
		size_t	start,
		size_t	stop,
		const CSeq_id *	seqid,
		unsigned int	options = eSplitLocOption_make_partial|eSplitLocOption_split_in_exon
	)

Definition at line 1833 of file loc_edit.cpp.

References CSeq_loc::Add(), 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, eExtreme_Positional, CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_loc::GetStart(), CSeq_loc_mix::IsReverseStrand(), CSeq_loc_equiv_Base::IsSet(), CSeq_loc_mix_Base::IsSet(), NormalizeLoc(), OkToAdjustLoc(), Ref(), CSeq_loc_Base::Reset(), CPacked_seqint_Base::Set(), CSeq_loc_equiv_Base::Set(), CSeq_loc_mix_Base::Set(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), SplitLocationForGap(), and CSeq_loc_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), CFeatGapInfo::Split(), and CFeatGapInfo::Trim().