Inheritance diagram for ExonModel:

Public Member Functions
StateType	getStateType () const

void	buildModel (const AnnoSequence *annoseq, int parIndex)

void	registerPars (Parameters *parameters)

void	printProbabilities (int parIndex, BaseCount bc, const char suffix=NULL)

void	viterbiForwardAndSampling (ViterbiMatrixType &, ViterbiMatrixType &, int, int, AlgorithmVariant, OptionListItem &)

void	processOvlpOption (ViterbiMatrixType &, ViterbiMatrixType &, AlgorithmVariant &, int state, int endOfPred, int beginOfBioExon, Double &maxProb, Double emiProb, Double &fwdsum, OptionsList *, OptionListItem &oli, int base) const

Double	emiProbUnderModel (int begin, int end) const

Double	endPartEmiProb (int end) const

Double	notEndPartEmiProb (int beginOfStart, int right, int frameOfRight, Feature *exonparts) const

void	initAlgorithms (Matrix< Double > &, int)

Public Member Functions inherited from StateModel
void	initPredecessors (Matrix< Double > &, int self)

virtual void	updateToLocalGCEach (Matrix< Double > &trans, int cur)

Static Public Member Functions
static void	storeGCPars (int idx)

static void	init ()

static void	resetPars ()

static void	updateToLocalGC (int from=-1, int to=-1)

static void	readProbabilities (int parIndex)

static void	readAllParameters ()

static double *	getCodonUsage ()

static void	resetModelCount ()

static int	getMaxStateLen ()

static void	setORF ()

Static Public Member Functions inherited from StateModel
static void	init ()

static StateModel *	newStateModelPtr (const char *path)

static void	determineShortPatterns (const vector< Integer > &patcounts, int k, int minCount)

static void	makeProbsFromCounts (vector< Double > &patprobs, const vector< Integer > &patcounts, int k, Double pseudocount, Boolean shorten=false)

static void	computeEmiFromPat (const vector< Double > &patprobs, vector< Double > &emiprobs, Integer k)

static void	prepareViterbi (const char *dna, int len, const vector< StateType > &stateMap)

static void	readProbabilities (int)

static void	resetPars ()

static void	updateToLocalGC (int idx, int from=-1, int to=-1)

static void	readAllParameters ()

static void	storeGCPars (int)

static void	resetModelCounts ()

static bool	isPossibleDSS (int pos)

static bool	isPossibleRDSS (int pos)

static bool	isPossibleASS (int pos)

static bool	isPossibleRASS (int pos)

static void	setSFC (SequenceFeatureCollection *psfc)

static void	setPP (PP::SubstateModel *mdl)

static void	setCountRegion (int from, int to)

static int	getActiveWindowStart (int)

static void	setGCIdx (int idx)

static void	setContentStairs (ContentStairs *stairs)

static int	getGCIdx (int at)

Static Public Attributes
static vector< Double >	lenDistSingle

static vector< Double >	lenDistInitial

static vector< Double >	lenDistInternal

static vector< Double >	lenDistTerminal

Additional Inherited Members
Protected Attributes inherited from StateModel
vector< Ancestor >	ancestor

Static Protected Attributes inherited from StateModel
static const vector< StateType > *	stateMap = NULL

static const char *	sequence = NULL

static int	dnalen = -1

static SequenceFeatureCollection *	seqFeatColl = NULL

static vector< Boolean > *	shortpattern = NULL

static PP::SubstateModel *	profileModel = NULL

static int	countStart = -1

static int	countEnd = -1

static int	activeWinLen = 1

static int	gcIdx = 0

static ContentStairs *	cs = NULL

Member Function Documentation

◆ buildModel()

void ExonModel::buildModel	(	const AnnoSequence *	annoseq,
		int	parIndex
	)

virtual

Implements StateModel.

◆ emiProbUnderModel()

Double ExonModel::emiProbUnderModel	(	int	begin,
		int	end
	)		const

virtual

Implements StateModel.

◆ getStateType()

StateType ExonModel::getStateType ( ) const

inlinevirtual

Implements StateModel.

◆ initAlgorithms()

void ExonModel::initAlgorithms	(	Matrix< Double > &	trans,
		int	cur
	)

virtual

Implements StateModel.

◆ printProbabilities()

void ExonModel::printProbabilities	(	int	parIndex,
		BaseCount *	bc,
		const char *	suffix = `NULL`
	)

virtual

Implements StateModel.

◆ registerPars()

void ExonModel::registerPars ( Parameters * parameters )

virtual

Reimplemented from StateModel.

◆ viterbiForwardAndSampling()

void ExonModel::viterbiForwardAndSampling	(	ViterbiMatrixType &	viterbi,
		ViterbiMatrixType &	forward,
		int	state,
		int	base,
		AlgorithmVariant	algovar,
		OptionListItem &	oli
	)

virtual

Implements StateModel.

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

include/exonmodel.hh
src/dummy.cc
src/exonmodel.cc
src/exontrain.cc

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Member Function Documentation

◆ buildModel()

◆ emiProbUnderModel()

◆ getStateType()

◆ initAlgorithms()

◆ printProbabilities()

◆ registerPars()

◆ viterbiForwardAndSampling()