This is the complete list of members for PP::SubstateModel, including all inherited members.

addHitSeqMatch(const HitSequence *hs, bool comp) (defined in PP::SubstateModel)	PP::SubstateModel	inline
addInternMatch(Position ppos, int beginOfBioExon, int endOfLastCodon, int endOfBioExon, bool comp) (defined in PP::SubstateModel)	PP::SubstateModel	inline
addPrefixMatch(Position ppos, int endOfLastCodon, int endOfBioExon, bool comp) (defined in PP::SubstateModel)	PP::SubstateModel	inline
addSuffixMatch(Position ppos, int beginOfFirstCodon, int beginOfBioExon, bool comp) (defined in PP::SubstateModel)	PP::SubstateModel	inline
advanceScores(int base) (defined in PP::SubstateModel)	PP::SubstateModel
allow_truncated (defined in PP::SubstateModel)	PP::SubstateModel
appendMatchesTo(list< Match > &target) (defined in PP::SubstateModel)	PP::SubstateModel	inline
blockCount() const (defined in PP::SubstateModel)	PP::SubstateModel	inline
blockNoOfB(int b, bool comp) const (defined in PP::SubstateModel)	PP::SubstateModel	inline
blockScores (defined in PP::SubstateModel)	PP::SubstateModel
blockSize(int b, bool comp) const (defined in PP::SubstateModel)	PP::SubstateModel	inline
clearLowScoring(ViterbiSubmapType &submap) (defined in PP::SubstateModel)	PP::SubstateModel
clearLowScoringSubstates(ViterbiColumnType &vit) (defined in PP::SubstateModel)	PP::SubstateModel	inline
currentResult (defined in PP::SubstateModel)	PP::SubstateModel
exhaustive_substates (defined in PP::SubstateModel)	PP::SubstateModel
getBlock(int b, bool comp) const (defined in PP::SubstateModel)	PP::SubstateModel	inline
getIntronBonus(int b, int i, int frame, bool comp) (defined in PP::SubstateModel)	PP::SubstateModel	inline
hitSeqColl (defined in PP::SubstateModel)	PP::SubstateModel
iBlockOfB(int b, bool comp) const (defined in PP::SubstateModel)	PP::SubstateModel	inline
initHitSequences() (defined in PP::SubstateModel)	PP::SubstateModel	inline
initScores() (defined in PP::SubstateModel)	PP::SubstateModel	inline
interBlockDist(int b, bool comp) const (defined in PP::SubstateModel)	PP::SubstateModel	inline
maxBlockSize (defined in PP::SubstateModel)	PP::SubstateModel
prfl (defined in PP::SubstateModel)	PP::SubstateModel
scoreAssOrRDss(ViterbiSubmapType &submap, bool complement, int firstBase, const Double &maxProb) (defined in PP::SubstateModel)	PP::SubstateModel
setStateStrands(const vector< StateType > &stateMap) (defined in PP::SubstateModel)	PP::SubstateModel	inlinestatic
SubstateModel(Profile &p) (defined in PP::SubstateModel)	PP::SubstateModel