LocARNA-1.9.2
LocARNA::RnaData Member List
This is the complete list of members for LocARNA::RnaData, including all inherited members.
arc_cutoff_prob() const LocARNA::RnaData
arc_prob(pos_type i, pos_type j) const LocARNA::RnaData
arc_prob_matrix_t typedefLocARNA::RnaData
arc_probs_begin() const LocARNA::RnaData [protected]
arc_probs_const_iterator typedefLocARNA::RnaData [protected]
arc_probs_end() const LocARNA::RnaData [protected]
ExtRnaDataImpl (defined in LocARNA::RnaData)LocARNA::RnaData [friend]
has_stacking() const LocARNA::RnaData
init_from_fixed_structure(const RnaStructure &structure, const PFoldParams &pfoldparams)LocARNA::RnaData [protected, virtual]
init_from_rna_ensemble(const RnaEnsemble &rna_ensemble, const PFoldParams &pfoldparams)LocARNA::RnaData [protected, virtual]
inloopprobs_ok() const LocARNA::RnaData [inline, 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(const std::string &filename)LocARNA::RnaData [protected, virtual]
read_pp(std::istream &in)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 typedefLocARNA::RnaData
stacked_arc_prob(pos_type i, pos_type j) const LocARNA::RnaData
write_pp(std::ostream &out, double p_outbpcut=0) const LocARNA::RnaData
write_size_info(std::ostream &out) const LocARNA::RnaData
~RnaData()LocARNA::RnaData [virtual]
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