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CGnomonEngine Class Reference

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#include <algo/gnomon/gnomon.hpp>

+ Collaboration diagram for CGnomonEngine:

List of all members.


struct  SGnomonEngineImplData

Public Member Functions

 CGnomonEngine (CConstRef< CHMMParameters > hmm_params, const CResidueVec &sequence, TSignedSeqRange range=TSignedSeqRange::GetWhole())
 ~CGnomonEngine ()
void ResetRange (TSignedSeqRange range)
void ResetRange (TSignedSeqPos from, TSignedSeqPos to)
const CResidueVecGetSeq () const
int GetGCcontent () const
int GetMinIntronLen () const
int GetMaxIntronLen () const
int GetMinIntergenicLen () const
double GetChanceOfIntronLongerThan (int l) const
void GetScore (CGeneModel &model, bool extend5p=false, bool obeystart=false) const
double SelectBestReadingFrame (const CGeneModel &model, const CEResidueVec &mrna, const CAlignMap &mrnamap, TIVec starts[3], TIVec stops[3], int &frame, int &best_start, int &best_stop, bool extend5p=true) const
double Run (bool repeats=true, bool leftwall=true, bool rightwall=true, double mpp=10)
double Run (const TGeneModelList &chains, bool repeats, bool leftwall, bool rightwall, bool leftanchor, bool rightanchor, double mpp, double consensuspenalty=BadScore(), const CGnomonAnnotator_Base::TIntMap &notbridgeable_gaps_len=CGnomonAnnotator_Base::TIntMap(), const CGnomonAnnotator_Base::TGgapInfo &ggapinfo=CGnomonAnnotator_Base::TGgapInfo())
CRef< objects::CSeq_annot > GetAnnot (const objects::CSeq_id &id)
list< CGeneModelGetGenes () const
TSignedSeqPos PartialModelStepBack (list< CGeneModel > &genes) const
void PrintInfo () const

Private Member Functions

 CGnomonEngine (const CGnomonEngine &value)
CGnomonEngineoperator= (const CGnomonEngine &value)
void CheckRange ()

Private Attributes

auto_ptr< SGnomonEngineImplDatam_data

Detailed Description

Definition at line 71 of file gnomon.hpp.

Constructor & Destructor Documentation

Definition at line 63 of file gnomon_engine.cpp.

Member Function Documentation

void CGnomonEngine::CheckRange ( ) [private]
CRef< CSeq_annot > CGnomonEngine::GetAnnot ( const objects::CSeq_id &  id)
void CGnomonEngine::GetScore ( CGeneModel model,
bool  extend5p = false,
bool  obeystart = false 
) const

Definition at line 136 of file gnomon_engine.cpp.

References m_data, and CGnomonEngine::SGnomonEngineImplData::m_seq.

Referenced by CGnomonAnnotator::Predict().

CGnomonEngine& CGnomonEngine::operator= ( const CGnomonEngine value) [private]
void CGnomonEngine::PrintInfo ( ) const
void CGnomonEngine::ResetRange ( TSignedSeqPos  from,
TSignedSeqPos  to 
) [inline]

Definition at line 77 of file gnomon.hpp.

References ResetRange().

Referenced by ResetRange().

double CGnomonEngine::Run ( bool  repeats = true,
bool  leftwall = true,
bool  rightwall = true,
double  mpp = 10 
double CGnomonEngine::Run ( const TGeneModelList chains,
bool  repeats,
bool  leftwall,
bool  rightwall,
bool  leftanchor,
bool  rightanchor,
double  mpp,
double  consensuspenalty = BadScore(),
const CGnomonAnnotator_Base::TIntMap notbridgeable_gaps_len = CGnomonAnnotator_Base::TIntMap(),
const CGnomonAnnotator_Base::TGgapInfo ggapinfo = CGnomonAnnotator_Base::TGgapInfo() 
double CGnomonEngine::SelectBestReadingFrame ( const CGeneModel model,
const CEResidueVec mrna,
const CAlignMap mrnamap,
TIVec  starts[3],
TIVec  stops[3],
int frame,
int best_start,
int best_stop,
bool  extend5p = true 
) const

Member Data Documentation

The documentation for this class was generated from the following files:
Modified on Fri Dec 19 11:43:37 2014 by rev. 426318