NCBI C++ ToolKit
Classes | Enumerations | Functions
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_locSeqLocExtend (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

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 
)

◆ CorrectIntervalOrder()

bool CorrectIntervalOrder ( CSeq_loc loc)

◆ ExtendPartialFeatureEnds()

bool ExtendPartialFeatureEnds ( CBioseq_Handle  bsh)

◆ FeatureAdjustForInsert()

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

◆ FeatureAdjustForTrim()

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

◆ IsExtendable()

bool IsExtendable ( const CSeq_feat cds,
CScope scope 
)

◆ PrintBestSeqId()

string PrintBestSeqId ( const CSeq_id sid,
CScope scope 
)

◆ PrintPntAndPntsUseBestID()

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

◆ PrintSeqIntUseBestID()

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

◆ ReverseComplementFeature()

void ReverseComplementFeature ( CSeq_feat feat,
CScope scope 
)

◆ ReverseComplementLocation()

void ReverseComplementLocation ( CSeq_loc loc,
CScope scope 
)

◆ SeqLocAdjustForInsert()

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

◆ SeqLocAdjustForTrim()

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

◆ SeqLocExtend()

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

◆ SeqLocPrintUseBestID()

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

◆ 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 
)
Modified on Fri Jun 14 16:49:05 2024 by modify_doxy.py rev. 669887