the class NAMGene is AUGUSTUS' entry point for the algorithms More...

#include <namgene.hh>

Public Member Functions
void	readModelProbabilities (int number=1)

StatePath *	getSampledPath (const char dna, const char seqname=NULL)

StatePath *	getViterbiPath (const char dna, const char seqname=NULL)

StatePath *	getTrainViterbiPath (const char dna, SequenceFeatureCollection sfc)

Transcript *	doViterbiPiecewise (SequenceFeatureCollection &sfc, AnnoSequence *annoseq, Strand strand, unsigned int &num_pieces)

Double	getEmissionProbability ()

const ViterbiMatrixType &	getForwardVariables ()

const ViterbiMatrixType &	getViterbiVariables ()

StateType	getStateType (int i)

int	getStateIndex (StateType type)

Double	getPathEmiProb (StatePath path, const char dna, SequenceFeatureCollection &sfc, int countStart=-1, int countEnd=-1)

void	setNeedForwardTable (bool b)

void	setPathAndProb (AnnoSequence *annoseq, FeatureCollection &extrinsicFeatures)

void	setAllTranscripts (list< Transcript * > *tl)

list< Transcript * > *	getAllTranscripts ()

void	getPrepareModels (const char *dna, int len)

Detailed Description

the class NAMGene is AUGUSTUS' entry point for the algorithms

Member Function Documentation

Transcript * NAMGene::doViterbiPiecewise	(	SequenceFeatureCollection &	sfc,
		AnnoSequence *	annoseq,
		Strand	strand,
		unsigned int &	num_pieces
	)

Predict the path through the HMM and compute the predicted genes. strand: plusstrand, minusstrand or bothstrands

const ViterbiMatrixType & NAMGene::getForwardVariables ( )

inline

Get the matrix with the variables calculated by the forward algorithm.

const ViterbiMatrixType & NAMGene::getViterbiVariables ( )

inline

Get the matrix with the variables calculated by the viterbi algorithm.

The documentation for this class was generated from the following files: