The intron model class. More...

#include <intronmodel.hh>

Inheritance diagram for IntronModel:

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	initAlgorithms (Matrix< Double > &, int)

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

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

Double	emiProbUnderModel (int begin, int end) const

Double	seqProb (int left, int right) const

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

Static Public Member Functions
static Double	dSSProb (int base, bool forwardStrand)

static Double	aSSProb (int base, bool forwardStrand)

static void	init ()

static void	resetPars ()

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

static void	readProbabilities (int parIndex)

static void	readAllParameters ()

static void	updateParameters (int idx)

static void	storeGCPars (int idx)

static Integer	getD ()

static double	getMAL ()

static void	resetModelCount ()

static double	getGeoProb ()

static Double	getAssMotifProbThreshold (double q)

static double	getMeanIntrLen ()

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 Integer	k = 4

static PatMMGroup	emiprobs

static PatMMGroup *	GCemiprobs = NULL

static BinnedMMGroup	dssBinProbs

static BinnedMMGroup	assBinProbs

static vector< Double >	lenDist

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

Detailed Description

The intron model class.

Author: Emmanouil Stafilarakis; Mario Stanke

Member Function Documentation

◆ buildModel()

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

virtual

Build all needed probabilities from the given gene set.

Parameters

annoseq A single linked list annotated sequences

Implements StateModel.

◆ emiProbUnderModel()

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

virtual

Implements StateModel.

◆ getStateType()

StateType IntronModel::getStateType ( ) const

inlinevirtual

Implements StateModel.

◆ initAlgorithms()

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

virtual

Implements StateModel.

◆ printProbabilities()

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

virtual

Print the wanted probabilities in files. The names of the files should be given with the Properties object /IntronModel/outfile

Implements StateModel.

◆ registerPars()

void IntronModel::registerPars ( Parameters * parameters )

virtual

Reimplemented from StateModel.

◆ updateToLocalGCEach()

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

virtual

Reimplemented from StateModel.

◆ viterbiForwardAndSampling()

void IntronModel::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/intronmodel.hh
src/dummy.cc
src/intronmodel.cc
src/introntrain.cc

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ buildModel()

◆ emiProbUnderModel()

◆ getStateType()

◆ initAlgorithms()

◆ printProbabilities()

◆ registerPars()

◆ updateToLocalGCEach()

◆ viterbiForwardAndSampling()