NcModel Class Reference

Model for non-protein-coding genes (nc) More...

#include <ncmodel.hh>

Inheritance diagram for NcModel:

Public Member Functions
StateType	getStateType () const
void	buildModel (const AnnoSequence *annoseq, int parIndex)
void	registerPars (Parameters *parameters)
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
void	precomputeTxEndProbs ()
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	init ()
static void	resetPars ()
static void	updateToLocalGC (int from=-1, int to=-1)
static void	readAllParameters ()
static void	resetModelCount ()
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 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

Model for non-protein-coding genes (nc)

Author

Mario Stanke

Member Function Documentation

buildModel()

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

virtual

No training of parameters. Other parameters are reused.

Implements StateModel.

emiProbUnderModel()

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

virtual

Implements StateModel.

getStateType()

StateType NcModel::getStateType ( ) const

inlinevirtual

Implements StateModel.

initAlgorithms()

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

virtual

Implements StateModel.

printProbabilities()

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

virtual

Implements StateModel.

registerPars()

void NcModel::registerPars ( Parameters *  parameters )

virtual

Reimplemented from StateModel.

viterbiForwardAndSampling()

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

virtual

Implements StateModel.

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

• include/ncmodel.hh
• src/ncmodel.cc