This is the complete list of members for LocARNA::Scoring, including all inherited members.

apply_unpaired_penalty()	LocARNA::Scoring
Arc typedef	LocARNA::Scoring
arcDel(const BasePairs__Arc &arc, bool gapAorB, bool stacked=false) const	LocARNA::Scoring
arcmatch(const ArcMatch &am, bool stacked=false) const	LocARNA::Scoring
arcmatch(const BasePairs__Arc &arcA, const BasePairs__Arc &arcB, bool stacked=false) const	LocARNA::Scoring
arcmatch_stacked(const ArcMatch &am) const	LocARNA::Scoring	inline
basematch(size_type i, size_type j) const	LocARNA::Scoring	inline
exclusion() const	LocARNA::Scoring	inline
exp_arcmatch(const ArcMatch &am) const	LocARNA::Scoring	inline
exp_basematch(size_type i, size_type j) const	LocARNA::Scoring	inline
exp_gapA(size_type posA) const	LocARNA::Scoring	inline
exp_gapB(size_type posB) const	LocARNA::Scoring	inline
exp_indel_opening() const	LocARNA::Scoring	inline
exp_indel_opening_loop() const	LocARNA::Scoring	inline
gapA(size_type posA) const	LocARNA::Scoring	inline
gapB(size_type posB) const	LocARNA::Scoring	inline
gapX(size_type alignedToGap, bool gapInA) const	LocARNA::Scoring	inline
indel_opening() const	LocARNA::Scoring	inline
indel_opening_loop() const	LocARNA::Scoring	inline
is_stackable_am(const ArcMatch &am) const	LocARNA::Scoring
is_stackable_arcA(const Arc &a) const	LocARNA::Scoring
is_stackable_arcB(const Arc &a) const	LocARNA::Scoring
lambda() const	LocARNA::Scoring	inline
loop_indel_score(const score_t score) const	LocARNA::Scoring	inline
modify_by_parameter(score_t lambda)	LocARNA::Scoring
prob_exp(size_type len) const	LocARNA::Scoring
Scoring(const Sequence &seqA, const Sequence &seqB, const RnaData &rna_dataA, const RnaData &rna_dataB, const ArcMatches &arc_matches, const MatchProbs *match_probs, const ScoringParams &params, bool exp_scores=false)	LocARNA::Scoring
stacking() const	LocARNA::Scoring	inline