NCBI C++ ToolKit
Classes | Functions
gnomon_seq.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <algo/gnomon/gnomon_model.hpp>
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Classes

class  CEResidueVec
 
class  CDoubleStrandSeq
 

Functions

void Convert (const CResidueVec &src, CEResidueVec &dst)
 
void Convert (const CEResidueVec &src, CResidueVec &dst)
 
void Convert (const CResidueVec &src, CDoubleStrandSeq &dst)
 
void ReverseComplement (const CEResidueVec &src, CEResidueVec &dst)
 
EResidue fromACGT (TResidue c)
 
TResidue toACGT (EResidue c)
 
void FindAllStarts (TIVec codons[], const CEResidueVec &mrna, const CAlignMap &mrnamap, TSignedSeqRange search_region, int fixed_frame)
 
void FindAllStops (TIVec codons[], const CEResidueVec &mrna, const CAlignMap &mrnamap, TSignedSeqRange search_region, int fixed_frame)
 
void FindStartsStops (const CGeneModel &model, const CEResidueVec &contig_seq, const CEResidueVec &mrna, const CAlignMap &mrnamap, TIVec starts[3], TIVec stops[3], int &frame, bool obeystart)
 
bool FindUpstreamStop (const vector< int > &stops, int start, int &stop)
 
bool FindFirstStart (const vector< int > &starts, int stop, int &start)
 

Function Documentation

◆ Convert() [1/3]

void Convert ( const CEResidueVec src,
CResidueVec dst 
)

Definition at line 58 of file gnomon_seq.cpp.

References i, len, and toACGT().

◆ Convert() [2/3]

void Convert ( const CResidueVec src,
CDoubleStrandSeq dst 
)

Definition at line 52 of file gnomon_seq.cpp.

References Convert(), eMinus, ePlus, and ReverseComplement().

◆ Convert() [3/3]

void Convert ( const CResidueVec src,
CEResidueVec dst 
)

Definition at line 43 of file gnomon_seq.cpp.

References fromACGT(), i, and len.

Referenced by Convert().

◆ FindAllStarts()

void FindAllStarts ( TIVec  codons[],
const CEResidueVec mrna,
const CAlignMap mrnamap,
TSignedSeqRange  search_region,
int  fixed_frame 
)

◆ FindAllStops()

void FindAllStops ( TIVec  codons[],
const CEResidueVec mrna,
const CAlignMap mrnamap,
TSignedSeqRange  search_region,
int  fixed_frame 
)

◆ FindFirstStart()

bool FindFirstStart ( const vector< int > &  starts,
int  stop,
int start 
)

Definition at line 298 of file gnomon_seq.cpp.

Referenced by CGnomonEngine::GetScore().

◆ FindStartsStops()

void FindStartsStops ( const CGeneModel model,
const CEResidueVec contig_seq,
const CEResidueVec mrna,
const CAlignMap mrnamap,
TIVec  starts[3],
TIVec  stops[3],
int frame,
bool  obeystart 
)

◆ FindUpstreamStop()

bool FindUpstreamStop ( const vector< int > &  stops,
int  start,
int stop 
)

Definition at line 287 of file gnomon_seq.cpp.

Referenced by CGnomonEngine::GetScore().

◆ fromACGT()

EResidue fromACGT ( TResidue  c)
inline

Definition at line 59 of file gnomon_seq.hpp.

References enA, enC, enG, enN, and enT.

Referenced by res_traits< EResidue >::_fromACGT(), Convert(), CCodingPropensity::GetScore(), and CSeqScores::Init().

◆ ReverseComplement()

void ReverseComplement ( const CEResidueVec src,
CEResidueVec dst 
)

Definition at line 67 of file gnomon_seq.cpp.

References i, k_toMinus, and len.

Referenced by CAlignMap::CAlignMap(), Convert(), and CAlignMap::EditedSequence().

◆ toACGT()

TResidue toACGT ( EResidue  c)
inline

Definition at line 81 of file gnomon_seq.hpp.

References enA, enC, enG, enN, and enT.

Referenced by Convert(), and CParse::GetGenes().

Modified on Thu Feb 22 17:13:14 2024 by modify_doxy.py rev. 669887