, including all inherited members.
| arc_cutoff_prob() const | LocARNA::RnaData | |
| arc_external_prob(pos_type i, pos_type j) const | LocARNA::ExtRnaData | |
| arc_in_loop_cutoff_prob() const | LocARNA::ExtRnaData | |
| arc_in_loop_prob(pos_type i, pos_type j, pos_type p, pos_type q) const | LocARNA::ExtRnaData | |
| arc_prob(pos_type i, pos_type j) const | LocARNA::RnaData | |
| arc_prob_matrix_t typedef | LocARNA::RnaData | |
| arc_probs_begin() const | LocARNA::RnaData | [protected] |
| arc_probs_const_iterator typedef | LocARNA::RnaData | [protected] |
| arc_probs_end() const | LocARNA::RnaData | [protected] |
| ExtRnaData(const RnaEnsemble &rna_ensemble, double p_bpcut, double p_bpilcut, double p_uilcut, double max_bps_length_ratio, double max_uil_length_ratio, double max_bpil_length_ratio, const PFoldParams &pfoldparams) | LocARNA::ExtRnaData | |
| ExtRnaData(const std::string &filename, double p_bpcut, double p_bpilcut, double p_uilcut, double max_bps_length_ratio, double max_uil_length_ratio, double max_bpil_length_ratio, const PFoldParams &pfoldparams) | LocARNA::ExtRnaData | |
| ExtRnaDataImpl (defined in LocARNA::ExtRnaData) | LocARNA::ExtRnaData | [friend] |
| has_stacking() const | LocARNA::RnaData | |
| init_from_fixed_structure(const RnaStructure &structure, const PFoldParams &pfoldparams) | LocARNA::ExtRnaData | [protected, virtual] |
| init_from_rna_ensemble(const RnaEnsemble &rna_ensemble, const PFoldParams &pfoldparams) | LocARNA::ExtRnaData | [protected, virtual] |
| inloopprobs_ok() const | LocARNA::ExtRnaData | [protected, virtual] |
| joint_arc_prob(pos_type i, pos_type j) const | LocARNA::RnaData | |
| length() const | LocARNA::RnaData | |
| mea_structure(double gamma=1.) const | LocARNA::RnaData | |
| multiple_alignment() const | LocARNA::RnaData | |
| pimpl_ | LocARNA::RnaData | [protected] |
| plist() const | LocARNA::RnaData | |
| prob_paired_downstream(pos_type i) const | LocARNA::RnaData | |
| prob_paired_upstream(pos_type i) const | LocARNA::RnaData | |
| prob_unpaired(pos_type i) const | LocARNA::RnaData | |
| read_autodetect(const std::string &filename, const PFoldParams &pfoldparams) | LocARNA::RnaData | [protected] |
| read_old_pp(const std::string &filename) | LocARNA::RnaData | [protected] |
| read_pp(std::istream &in) | LocARNA::ExtRnaData | [protected, virtual] |
| LocARNA::RnaData::read_pp(const std::string &filename) | LocARNA::RnaData | [protected, virtual] |
| read_ps(const std::string &filename) | LocARNA::RnaData | [protected] |
| RnaData(const RnaEnsemble &rna_ensemble, double p_bpcut, double max_bps_length_ratio, const PFoldParams &pfoldparams) | LocARNA::RnaData | |
| RnaData(const std::string &filename, double p_bpcut, double max_bps_length_ratio, const PFoldParams &pfoldparams) | LocARNA::RnaData | |
| RnaData(const RnaData &rna_dataA, const RnaData &rna_dataB, const Alignment &alignment, double p_expA, double p_expB, bool only_local=false) | LocARNA::RnaData | |
| RnaData(double p_bpcut, size_t max_bp_span) | LocARNA::RnaData | [explicit, protected] |
| RnaDataImpl (defined in LocARNA::RnaData) | LocARNA::RnaData | [friend] |
| sequence() const | LocARNA::RnaData | |
| set_anchors(const SequenceAnnotation &anchors) | LocARNA::RnaData | |
| size_type typedef | LocARNA::RnaData | |
| stacked_arc_prob(pos_type i, pos_type j) const | LocARNA::RnaData | |
| unpaired_external_prob(pos_type k) const | LocARNA::ExtRnaData | |
| unpaired_in_loop_cutoff_prob() const | LocARNA::ExtRnaData | |
| unpaired_in_loop_prob(pos_type k, pos_type p, pos_type q) const | LocARNA::ExtRnaData | |
| write_pp(std::ostream &out, double p_outbpcut=0, double p_outbpilcut=0, double p_outuilcut=0) const | LocARNA::ExtRnaData | |
| LocARNA::RnaData::write_pp(std::ostream &out, double p_outbpcut=0) const | LocARNA::RnaData | |
| write_size_info(std::ostream &out) const | LocARNA::ExtRnaData | |
| ~ExtRnaData() | LocARNA::ExtRnaData | |
| ~RnaData() | LocARNA::RnaData | [virtual] |
1.7.6.1
