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LocARNA-2.0.0
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This is the complete list of members for LocARNA::PFScoring< T >, including all inherited members.
| apply_unpaired_penalty() | LocARNA::Scoring | |
| Arc typedef | LocARNA::Scoring | |
| arc_matches() const | LocARNA::Scoring | inline |
| arc_matches_ | LocARNA::Scoring | protected |
| arcDel(const BasePairs__Arc &arc, 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 |
| boltzmann_weight(score_t s) const (defined in LocARNA::PFScoring< T >) | LocARNA::PFScoring< T > | inlineprotected |
| exclusion() const | LocARNA::Scoring | inline |
| exp_arcmatch(const ArcMatch &am) const | LocARNA::PFScoring< T > | inline |
| exp_basematch(size_type i, size_type j) const | LocARNA::PFScoring< T > | inline |
| exp_gapA(size_type posA) const | LocARNA::PFScoring< T > | inline |
| exp_gapB(size_type posB) const | LocARNA::PFScoring< T > | inline |
| exp_indel_opening() const | LocARNA::PFScoring< T > | inline |
| exp_indel_opening_loop() const | LocARNA::PFScoring< T > | inline |
| gapA(size_type posA) const | LocARNA::Scoring | inline |
| gapB(size_type posB) const | LocARNA::Scoring | inline |
| gapcost_tabA | LocARNA::Scoring | protected |
| gapcost_tabB | LocARNA::Scoring | protected |
| gapX(size_type alignedToGap) const | LocARNA::Scoring | inline |
| gapX(size_type alignedToGap) const (defined in LocARNA::Scoring) | LocARNA::Scoring | inline |
| gapX(size_type alignedToGap) const (defined in LocARNA::Scoring) | LocARNA::Scoring | inline |
| identity | LocARNA::Scoring | protected |
| 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 |
| lambda_ | LocARNA::Scoring | protected |
| loop_indel_score(const score_t score) const | LocARNA::Scoring | inline |
| match_probs | LocARNA::Scoring | protected |
| modify_by_parameter(score_t lambda) | LocARNA::Scoring | |
| params | LocARNA::Scoring | protected |
| pf_score_t typedef (defined in LocARNA::PFScoring< T >) | LocARNA::PFScoring< T > | |
| PFScoreMatrix typedef | LocARNA::PFScoring< T > | |
| PFScoreVector typedef | LocARNA::PFScoring< T > | |
| PFScoring(const Sequence &seqA, const Sequence &seqB, const RnaData &rna_dataA, const RnaData &rna_dataB, const ArcMatches &arc_matches, const MatchProbs *match_probs, const ScoringParams ¶ms) | LocARNA::PFScoring< T > | |
| precompute_exp_gapcost() | LocARNA::PFScoring< T > | protected |
| precompute_exp_sigma() | LocARNA::PFScoring< T > | protected |
| precompute_gapcost() | LocARNA::Scoring | protected |
| precompute_sequence_identities() (defined in LocARNA::Scoring) | LocARNA::Scoring | protected |
| precompute_sigma() | LocARNA::Scoring | protected |
| precompute_weights() | LocARNA::Scoring | protected |
| precompute_weights(const RnaData &rna_data, const BasePairs &bps, double exp_prob, std::vector< score_t > &weights, std::vector< score_t > &stack_weights) | LocARNA::Scoring | protected |
| prob_exp(size_type len) const | LocARNA::Scoring | |
| probToWeight(double p, double prob_exp) const | LocARNA::Scoring | protected |
| ribosum_arcmatch_prob(const Arc &arcA, const Arc &arcB) const | LocARNA::Scoring | protected |
| riboX_arcmatch_score(const Arc &arcA, const Arc &arcB) const | LocARNA::Scoring | protected |
| rna_dataA | LocARNA::Scoring | protected |
| rna_dataB | LocARNA::Scoring | protected |
| round2score(double d) const | LocARNA::Scoring | inlineprotected |
| 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 ¶ms) | LocARNA::Scoring | |
| seqA | LocARNA::Scoring | protected |
| seqB | LocARNA::Scoring | protected |
| sigma_(int i, int j) const | LocARNA::Scoring | protected |
| sigma_tab | LocARNA::Scoring | protected |
| stack_weightsA (defined in LocARNA::Scoring) | LocARNA::Scoring | protected |
| stack_weightsB (defined in LocARNA::Scoring) | LocARNA::Scoring | protected |
| stacking() const | LocARNA::Scoring | inline |
| subtract(std::vector< score_t > &v, score_t x) const | LocARNA::Scoring | protected |
| subtract(Matrix< score_t > &m, score_t x) const | LocARNA::Scoring | protected |
| weightsA (defined in LocARNA::Scoring) | LocARNA::Scoring | protected |
| weightsB (defined in LocARNA::Scoring) | LocARNA::Scoring | protected |
1.9.1