Inheritance diagram for PP::ExonScorer:

Public Member Functions
void	newFirstCodon (int beginOfBioExon)

virtual void	scoreFirst (ViterbiColumnType &col, int predState, const Double &transEmiProb)=0

virtual void	scoreInternal (ViterbiColumnType &col, int predState, const Double &transEmiProb)=0

void	score (ViterbiColumnType &col, int predState, const Double &transEmiProb)

virtual void	postProcessing (const Double &maxProb)=0

virtual void	exportSubstates (ViterbiSubmapType &)

virtual SubstateId	getPredSubstate ()

virtual bool	hasNewMax ()

virtual void	addMatches (int, int)

bool	validSize ()

Protected Member Functions
	ExonScorer (SubstateModel &model, int endOfBioExon, StateType type)

int	blockCount () const

int	blockSize (int b) const

const Block &	getBlock (int b) const

bool	exceedsBlock (Position ppos) const

DistanceType	interBlockDist (int b) const

DistanceType	interBlockFullDist (int b) const

Range	interBlockRange (int b) const

Range	interBlockFullRange (int b) const

Position	asNextPos (Position ppos)

Protected Attributes
void(ExonScorer::*	scoreFunPtr )(ViterbiColumnType &, int predState, const Double &)

bool	complement

SubstateModel &	mdl

vector< BlockScoreType > &	blockScores

int	aa_count

int	beginOfFirstCodon

int	endOfLastCodon

HitSequenceCollection *	currentHSColl

bool	is_active

int	endStateOffset

bool	backward_mode

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

Public Member Functions

Protected Member Functions