This is the complete list of members for StateModel, including all inherited members.

activeWinLen (defined in StateModel)	StateModel	protectedstatic
ancestor (defined in StateModel)	StateModel	protected
buildModel(const AnnoSequence *annoseq, int parIndex)=0 (defined in StateModel)	StateModel	pure virtual
computeEmiFromPat(const vector< Double > &patprobs, vector< Double > &emiprobs, Integer k) (defined in StateModel)	StateModel	static
countEnd (defined in StateModel)	StateModel	protectedstatic
countStart (defined in StateModel)	StateModel	protectedstatic
cs (defined in StateModel)	StateModel	protectedstatic
determineShortPatterns(const vector< Integer > &patcounts, int k, int minCount) (defined in StateModel)	StateModel	static
dnalen (defined in StateModel)	StateModel	protectedstatic
emiProbUnderModel(int, int) const =0 (defined in StateModel)	StateModel	pure virtual
gcIdx (defined in StateModel)	StateModel	protectedstatic
getActiveWindowStart(int) (defined in StateModel)	StateModel	static
getGCIdx(int at) (defined in StateModel)	StateModel	inlinestatic
getStateType() const =0 (defined in StateModel)	StateModel	pure virtual
init() (defined in StateModel)	StateModel	static
initAlgorithms(Matrix< Double > &, int)=0 (defined in StateModel)	StateModel	pure virtual
initPredecessors(Matrix< Double > &, int self) (defined in StateModel)	StateModel
isPossibleASS(int pos) (defined in StateModel)	StateModel	inlinestatic
isPossibleDSS(int pos) (defined in StateModel)	StateModel	inlinestatic
isPossibleRASS(int pos) (defined in StateModel)	StateModel	inlinestatic
isPossibleRDSS(int pos) (defined in StateModel)	StateModel	inlinestatic
makeProbsFromCounts(vector< Double > &patprobs, const vector< Integer > &patcounts, int k, Double pseudocount, Boolean shorten=false) (defined in StateModel)	StateModel	static
newStateModelPtr(const char *path)	StateModel	static
prepareViterbi(const char *dna, int len, const vector< StateType > &stateMap) (defined in StateModel)	StateModel	static
printProbabilities(int zusNumber=1, BaseCount bc=NULL, const char suffix=NULL)=0 (defined in StateModel)	StateModel	pure virtual
profileModel (defined in StateModel)	StateModel	protectedstatic
readAllParameters() (defined in StateModel)	StateModel	static
readProbabilities(int) (defined in StateModel)	StateModel	static
registerPars(Parameters *parameters) (defined in StateModel)	StateModel	inlinevirtual
resetModelCounts() (defined in StateModel)	StateModel	static
resetPars() (defined in StateModel)	StateModel	static
seqFeatColl (defined in StateModel)	StateModel	protectedstatic
sequence (defined in StateModel)	StateModel	protectedstatic
setContentStairs(ContentStairs *stairs) (defined in StateModel)	StateModel	inlinestatic
setCountRegion(int from, int to) (defined in StateModel)	StateModel	inlinestatic
setGCIdx(int idx) (defined in StateModel)	StateModel	inlinestatic
setPP(PP::SubstateModel *mdl) (defined in StateModel)	StateModel	inlinestatic
setSFC(SequenceFeatureCollection *psfc) (defined in StateModel)	StateModel	inlinestatic
shortpattern (defined in StateModel)	StateModel	protectedstatic
stateMap (defined in StateModel)	StateModel	protectedstatic
StateModel() (defined in StateModel)	StateModel	inlineprotected
storeGCPars(int) (defined in StateModel)	StateModel	static
updateToLocalGC(int idx, int from=-1, int to=-1) (defined in StateModel)	StateModel	static
updateToLocalGCEach(Matrix< Double > &trans, int cur) (defined in StateModel)	StateModel	inlinevirtual
viterbiForwardAndSampling(ViterbiMatrixType &, ViterbiMatrixType &, int, int, AlgorithmVariant, OptionListItem &)=0 (defined in StateModel)	StateModel	pure virtual
~StateModel() (defined in StateModel)	StateModel	inlinevirtual