NCBI C++ ToolKit
Functions | Variables
nucprot.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <algo/align/prosplign/prosplign_exception.hpp>
#include "nucprot.hpp"
#include "intron.hpp"
#include "Info.hpp"
#include "BackAlignInfo.hpp"
#include "Ali.hpp"
#include "AlignInfo.hpp"
#include "scoring.hpp"
#include <util/tables/raw_scoremat.h>
+ Include dependency graph for nucprot.cpp:

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Functions

int FrAlign (const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &, const CSubstMatrix &matrix)
 
int FindFGapIntronNog (const CProSplignInterrupt &interrupt, vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, bool &left_gap, bool &right_gap, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)
 
int FindIGapIntrons (const CProSplignInterrupt &interrupt, vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)
 
void FrBackAlign (CBackAlignInfo &bi, CAli &ali)
 
int FrAlignFNog1 (const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix, bool left_gap, bool right_gap)
 
int AlignFNog (const CProSplignInterrupt &interrupt, CTBackAlignInfo< CBMode > &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)
 
void BackAlignNog (CTBackAlignInfo< CBMode > &bi, CAli &ali)
 

Variables

const int infinity = numeric_limits<int>::min()/3
 

Function Documentation

◆ AlignFNog()

int AlignFNog ( const CProSplignInterrupt interrupt,
CTBackAlignInfo< CBMode > &  bi,
const PSEQ pseq,
const CNSeq nseq,
const CProSplignScaledScoring scoring,
const CSubstMatrix matrix 
)

◆ BackAlignNog()

void BackAlignNog ( CTBackAlignInfo< CBMode > &  bi,
CAli ali 
)

◆ FindFGapIntronNog()

int FindFGapIntronNog ( const CProSplignInterrupt interrupt,
vector< pair< int, int > > &  igi,
const PSEQ pseq,
const CNSeq nseq,
bool left_gap,
bool right_gap,
const CProSplignScaledScoring scoring,
const CSubstMatrix matrix 
)

◆ FindIGapIntrons()

int FindIGapIntrons ( const CProSplignInterrupt interrupt,
vector< pair< int, int > > &  igi,
const PSEQ pseq,
const CNSeq nseq,
int  g,
int  e,
int  f,
const CProSplignScaledScoring scoring,
const CSubstMatrix matrix 
)

◆ FrAlign()

int FrAlign ( const CProSplignInterrupt interrupt,
CBackAlignInfo bi,
const PSEQ pseq,
const CNSeq nseq,
int  g,
int  e,
int  f,
const CProSplignScaledScoring scoring,
const CSubstMatrix matrix 
)

◆ FrAlignFNog1()

int FrAlignFNog1 ( const CProSplignInterrupt interrupt,
CBackAlignInfo bi,
const PSEQ pseq,
const CNSeq nseq,
const CProSplignScaledScoring scoring,
const CSubstMatrix matrix,
bool  left_gap,
bool  right_gap 
)

◆ FrBackAlign()

void FrBackAlign ( CBackAlignInfo bi,
CAli ali 
)

Variable Documentation

◆ infinity

const int infinity = numeric_limits<int>::min()/3
Modified on Fri Mar 01 10:09:05 2024 by modify_doxy.py rev. 669887