IGenicModel Class Reference

intergenic region More...

#include <igenicmodel.hh>

Inheritance diagram for IGenicModel:

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
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	setSFC (SequenceFeatureCollection *sfc)
static void	resetPars ()
static void	updateToLocalGC (int from, int to)
static void	readProbabilities (int zusNumber)
static void	readAllParameters ()
static void	storeGCPars (int idx)
static double	getGeoProb ()
static vector< double >	getNucleotideProbs ()
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

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

intergenic region

Author

Mario Stanke

Member Function Documentation

buildModel()

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

virtual

Implements StateModel.

emiProbUnderModel()

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

virtual

Implements StateModel.

getStateType()

StateType IGenicModel::getStateType ( ) const

inlinevirtual

Implements StateModel.

initAlgorithms()

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

virtual

Implements StateModel.

printProbabilities()

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

virtual

Implements StateModel.

registerPars()

void IGenicModel::registerPars ( Parameters *  parameters )

virtual

Reimplemented from StateModel.

viterbiForwardAndSampling()

void IGenicModel::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/igenicmodel.hh
• src/dummy.cc
• src/igenicmodel.cc
• src/igenictrain.cc