NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
splice_problems.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <corelib/ncbi_autoinit.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objmgr/util/feature.hpp>
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Classes

class  CSpliceProblems
 

Typedefs

typedef Char(& TSpliceSite)[2]
 
typedef Char const (& TConstSpliceSite)[2]
 

Functions

bool CheckAdjacentSpliceSites (const string &signature, ENa_strand strand, TConstSpliceSite donor, TConstSpliceSite acceptor)
 
bool CheckSpliceSite (const string &signature, ENa_strand strand, TConstSpliceSite site)
 
bool CheckIntronSpliceSites (ENa_strand strand, TConstSpliceSite donor, TConstSpliceSite acceptor)
 
bool CheckIntronDonor (ENa_strand strand, TConstSpliceSite donor)
 
bool CheckIntronAcceptor (ENa_strand strand, TConstSpliceSite acceptor)
 

Variables

const string kSpliceSiteGTAG = "GT-AG"
 
const string kSpliceSiteGCAG = "GC-AG"
 
const string kSpliceSiteATAC = "AT-AC"
 
const string kSpliceSiteGT = "GT"
 
const string kSpliceSiteGC = "GC"
 
const string kSpliceSiteAG = "AG"
 

Typedef Documentation

◆ TConstSpliceSite

typedef Char const(& TConstSpliceSite)[2]

Definition at line 153 of file splice_problems.hpp.

◆ TSpliceSite

typedef Char(& TSpliceSite)[2]

Definition at line 95 of file splice_problems.hpp.

Function Documentation

◆ CheckAdjacentSpliceSites()

bool CheckAdjacentSpliceSites ( const string signature,
ENa_strand  strand,
TConstSpliceSite  donor,
TConstSpliceSite  acceptor 
)

◆ CheckIntronAcceptor()

bool CheckIntronAcceptor ( ENa_strand  strand,
TConstSpliceSite  acceptor 
)

Definition at line 746 of file splice_problems.cpp.

References CheckSpliceSite(), and kSpliceSiteAG.

Referenced by CIntronValidator::Validate().

◆ CheckIntronDonor()

bool CheckIntronDonor ( ENa_strand  strand,
TConstSpliceSite  donor 
)

Definition at line 740 of file splice_problems.cpp.

References CheckSpliceSite(), kSpliceSiteGC, and kSpliceSiteGT.

Referenced by CIntronValidator::Validate().

◆ CheckIntronSpliceSites()

bool CheckIntronSpliceSites ( ENa_strand  strand,
TConstSpliceSite  donor,
TConstSpliceSite  acceptor 
)

◆ CheckSpliceSite()

bool CheckSpliceSite ( const string signature,
ENa_strand  strand,
TConstSpliceSite  site 
)

Variable Documentation

◆ kSpliceSiteAG

const string kSpliceSiteAG = "AG"

◆ kSpliceSiteATAC

const string kSpliceSiteATAC = "AT-AC"

◆ kSpliceSiteGC

const string kSpliceSiteGC = "GC"

◆ kSpliceSiteGCAG

const string kSpliceSiteGCAG = "GC-AG"

◆ kSpliceSiteGT

const string kSpliceSiteGT = "GT"

◆ kSpliceSiteGTAG

const string kSpliceSiteGTAG = "GT-AG"
Modified on Wed Feb 21 09:56:38 2024 by modify_doxy.py rev. 669887