Untranslated Region Model. More...

#include <utrmodel.hh>

Inheritance diagram for UtrModel:

Public Member Functions
StateType	getStateType () const

void	buildModel (const AnnoSequence *annoseq, int parIndex)

void	registerPars (Parameters *parameters)

void	processStates (const Gene *gene)

void	process5SingleExon (const State *exon, bool withLen=true)

void	process5InitialExon (const State *exon, bool withLen=true)

void	process5InternalExon (const State *exon)

void	process5TerminalExon (const State *exon)

void	process5Intron (int begin, int end)

void	process3SingleExon (const State *exon, bool withLen=true)

void	process3InitialExon (const State *exon, bool withLen=true)

void	process3InternalExon (const State *exon)

void	process3TerminalExon (const State *exon, bool withLen)

void	process3Intron (int begin, int end)

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

void	initAlgorithms (Matrix< Double > &, int)

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

Double	emiProbUnderModel (int begin, int end) const

Double	endPartEmiProb (int begin, int end, int endOfBioExon) const

Double	notEndPartEmiProb (int begin, int end, int endOfBioExon, Feature *exonparts) const

void	getEndPositions (int end, int &beginOfEndPart, int &endOfBioExon) const

Double	tssupSeqProb (int left, int right, bool reverse) const

Double	tssProb (int left) const

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	computeTtsProbs (int from, int to)

static void	init ()

static void	resetPars ()

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

static void	clearSegProbs ()

static void	readProbabilities (int zusNumber)

static void	readAllParameters ()

static void	storeGCPars (int idx)

static void	resetModelCount ()

static void	setTtsSpacing (int spacing)

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)

Additional Inherited Members
Protected Member Functions inherited from StateModel
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

Untranslated Region Model.

Author: Mario Stanke

Member Function Documentation

◆ buildModel()

void UtrModel::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 UtrModel::emiProbUnderModel	(	int	begin,
		int	end ) const

virtual

Implements StateModel.

◆ getStateType()

StateType UtrModel::getStateType ( ) const

inlinevirtual

Implements StateModel.

◆ initAlgorithms()

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

virtual

Implements StateModel.

◆ printProbabilities()

void UtrModel::printProbabilities	(	int	zusNumber,
		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 /UtrModel/outfile

Implements StateModel.

◆ registerPars()

void UtrModel::registerPars ( Parameters * parameters )

virtual

Reimplemented from StateModel.

◆ viterbiForwardAndSampling()

void UtrModel::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/utrmodel.hh
src/dummy.cc
src/utrmodel.cc
src/utrtrain.cc

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ buildModel()

◆ emiProbUnderModel()

◆ getStateType()

◆ initAlgorithms()

◆ printProbabilities()

◆ registerPars()

◆ viterbiForwardAndSampling()