NAMGene Class Reference

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

Author

Mario Stanke

Emmanouil Stafilarakis

Member Function Documentation

doViterbiPiecewise()

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

getForwardVariables()

const ViterbiMatrixType & NAMGene::getForwardVariables ( )

inline

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

Returns

The forward variables.

See also

forwardAlgorithm

getViterbiVariables()

const ViterbiMatrixType & NAMGene::getViterbiVariables ( )

inline

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

Returns

The viterbi variables.

See also

viterbiAlgorithm

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

• include/namgene.hh
• src/namgene.cc