NCBI C++ ToolKit
Classes | Enumerations | Functions
nucprot.hpp File Reference
#include <corelib/ncbi_limits.hpp>
#include <algorithm>
#include <sstream>
#include "NSeq.hpp"
#include "PSeq.hpp"
#include "BackAlignInfo.hpp"
#include "scoring.hpp"
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <algo/align/prosplign/prosplign_exception.hpp>
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Classes

struct  CBMode
 
class  CTranslationTable
 
class  CSubstMatrix
 Substitution Matrix for Scoring Amino-Acid Alignments. More...
 
class  CFastIScore
 
class  CProSplignInterrupt
 

Enumerations

enum  EWMode {
  eD , eV , eH , eH1 ,
  eH2 , eH3 , eFV , eFH ,
  eS
}
 

Functions

void ReadFasta (vector< char > &pseq, istream &ifs, bool is_nuc, string &id)
 
void ReadNucFa (CNSeq &seq, const string &fname, string &id)
 
void ReadProtFa (PSEQ &seq, const string &fname, string &id)
 
int FrAlignFNog1 (const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix, bool left_gap=false, bool right_gap=false)
 
void FrBackAlign (CBackAlignInfo &bi, CAli &ali)
 
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)
 
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)
 
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)
 

Enumeration Type Documentation

◆ EWMode

enum EWMode
Enumerator
eD 
eV 
eH 
eH1 
eH2 
eH3 
eFV 
eFH 
eS 

Definition at line 54 of file nucprot.hpp.

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 = false,
bool  right_gap = false 
)

◆ FrBackAlign()

void FrBackAlign ( CBackAlignInfo bi,
CAli ali 
)

◆ ReadFasta()

void ReadFasta ( vector< char > &  pseq,
istream &  ifs,
bool  is_nuc,
string id 
)

◆ ReadNucFa()

void ReadNucFa ( CNSeq seq,
const string fname,
string id 
)

◆ ReadProtFa()

void ReadProtFa ( PSEQ seq,
const string fname,
string id 
)
Modified on Tue Jul 23 17:56:57 2024 by modify_doxy.py rev. 669887