Inheritance diagram for PP::SingleTargetExonScorer:

Public Member Functions
	SingleTargetExonScorer (SubstateModel &model, StateType etype, int endOfBioExon)

	SingleTargetExonScorer (SubstateModel &model, StateType etype, SubstateId substate, int endofBioExon, int ORFleft)

void	calcAllowedDist (bool is_last)

void	createHitSequences (int ORFleft)

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

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

virtual void	postProcessing (const Double &mainProb)

virtual void	exportSubstates (ViterbiSubmapType &)

virtual SubstateId	getPredSubstate ()

virtual bool	hasNewMax ()

virtual void	addMatches (int beginOfBioExon, int endOfBioExon)

Public Member Functions inherited from PP::ExonScorer
void	newFirstCodon (int beginOfBioExon)

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

bool	validSize ()

Additional Inherited Members
Protected Member Functions inherited from PP::ExonScorer
	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 inherited from PP::ExonScorer
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

Member Function Documentation

◆ addMatches()

virtual void PP::SingleTargetExonScorer::addMatches	(	int	beginOfBioExon,
		int	endOfBioExon )

inlinevirtual

Reimplemented from PP::ExonScorer.

void SingleTargetExonScorer::exportSubstates ( ViterbiSubmapType & targetVit )

virtual

Reimplemented from PP::ExonScorer.

virtual SubstateId PP::SingleTargetExonScorer::getPredSubstate ( )

inlinevirtual

Reimplemented from PP::ExonScorer.

virtual bool PP::SingleTargetExonScorer::hasNewMax ( )

inlinevirtual

Reimplemented from PP::ExonScorer.

void SingleTargetExonScorer::postProcessing ( const Double & mainProb )

virtual

void SingleTargetExonScorer::scoreFirst	(	ViterbiColumnType &	col,
		int	predState,
		const Double &	transEmiProb )

virtual

void SingleTargetExonScorer::scoreInternal	(	ViterbiColumnType &	col,
		int	predState,
		const Double &	transEmiProb )

virtual

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