This is the base interface class common to all state model classes (ExonModel, IntronModel, IGenicModel, UTRModel) More...

#include <statemodel.hh>

Inheritance diagram for StateModel:

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

virtual void	registerPars (Parameters *parameters)

virtual void	buildModel (const AnnoSequence *annoseq, int parIndex)=0

virtual void	printProbabilities (int zusNumber=1, BaseCount bc=NULL, const char suffix=NULL)=0

virtual StateType	getStateType () const =0

virtual void	viterbiForwardAndSampling (ViterbiMatrixType &, ViterbiMatrixType &, int, int, AlgorithmVariant, OptionListItem &)=0

virtual Double	emiProbUnderModel (int, int) const =0

virtual void	initAlgorithms (Matrix< Double > &, int)=0

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

Static Public Member Functions
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)

Protected Attributes
vector< Ancestor >	ancestor

Static Protected Attributes
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

Detailed Description

This is the base interface class common to all state model classes (ExonModel, IntronModel, IGenicModel, UTRModel)

Author: Emmanouil Stafilarakis; Mario Stanke

Member Function Documentation

◆ buildModel()

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

pure virtual

Implemented in IntronModel, NcModel, and UtrModel.

◆ newStateModelPtr()

StateModel * StateModel::newStateModelPtr ( const char * path )

static

newStateModelPtr: Get a pointer to a StateModel object.

creates a new StateModel descendant; the type is determined by by the string path, currently one of: intronmodel, exonmodel, igenicmodel, utrmodel, ncmodel

◆ printProbabilities()

virtual void StateModel::printProbabilities	(	int	zusNumber = `1`,
		BaseCount *	bc = `NULL`,
		const char *	suffix = `NULL`
	)

pure virtual

Implemented in IntronModel, and UtrModel.

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

include/statemodel.hh
src/statemodel.cc

Public Member Functions

Static Public Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Function Documentation

◆ buildModel()

◆ newStateModelPtr()

◆ printProbabilities()