1 #ifndef LOCARNA_RNA_DATA_IMPL_HH 2 #define LOCARNA_RNA_DATA_IMPL_HH 10 #include "sequence.hh" 14 class MultipleAlignment;
155 bool stacking)
const;
201 double p_expB)
const;
207 typedef std::pair<KEY,arc_prob_matrix_t::value_t> kvpair_t;
209 typedef std::vector<kvpair_t> vec_t;
213 bool comp(
const kvpair_t &x,
const kvpair_t &y) {
214 return x.second>y.second;
232 #endif // LOCARNA_RNA_DATA_IMPL_HH represent sparsified data of RNA ensemble
Definition: rna_data.hh:42
MultipleAlignment sequence_
the sequence
Definition: rna_data_impl.hh:30
void init_as_consensus_dot_plot(const Alignment::edges_t &edges, const RnaData &rna_dataA, const RnaData &rna_dataB, double p_expA, double p_expB, bool stacking)
Initialize as consensus of two aligned RNAs.
Definition: rna_data.cc:1498
pair of vector of alignment edges
Definition: alignment.hh:63
void drop_worst_bps(size_t keep)
Drop base pairs with lowest probability.
Definition: rna_data.cc:1587
RnaData::arc_prob_matrix_t arc_prob_matrix_t
type for matrix of arc probabilities
Definition: rna_data_impl.hh:25
double p_bpcut_
cutoff probabilitiy for base pair
Definition: rna_data_impl.hh:33
RnaDataImpl(RnaData *self, const RnaData &rna_dataA, const RnaData &rna_dataB, const Alignment::edges_t &alignment, double p_expA, double p_expB)
Construct as consensus of two aligned RNAs.
Definition: rna_data.cc:108
Definition: aligner.cc:17
std::istream & read_pp_sequence(std::istream &in)
read sequence section of pp-format
Definition: rna_data.cc:1039
Implementation of RnaData.
Definition: rna_data_impl.hh:22
std::ostream & write_pp_arc_probabilities(std::ostream &out, double p_outbpcut, bool stacking) const
write section of base pair probabilities of pp-format
Definition: rna_data.cc:1331
Parameters for partition folding.
Definition: pfold_params.hh:19
std::ostream & write_pp_sequence(std::ostream &out) const
write section of base pair probabilities of pp-format
Definition: rna_data.cc:1286
void init_from_rna_ensemble(const RnaEnsemble &rna_ensemble, const PFoldParams &pfoldparams)
initialize from rna ensemble
Definition: rna_data.cc:528
std::istream & read_pp_arc_probabilities(std::istream &in)
read section of base pair probabilities of pp-format
Definition: rna_data.cc:1065
arc_prob_matrix_t arc_2_probs_
Definition: rna_data_impl.hh:49
RnaData * self_
Definition: rna_data_impl.hh:27
Represents the raw structure ensemble data for an RNA.
Definition: rna_ensemble.hh:40
void init_from_fixed_structure(const SequenceAnnotation &structure, bool stacking)
initialize from fixed structure
Definition: rna_data.cc:395
double consensus_probability(double pA, double pB, size_t sizeA, size_t sizeB, double p_expA, double p_expB) const
Consensus probability.
Definition: rna_data.cc:1564
Annotation of a sequence.
Definition: sequence_annotation.hh:24
arc_prob_matrix_t arc_probs_
Definition: rna_data_impl.hh:40
Definition: rna_data_impl.hh:205
Represents a multiple alignment.
Definition: multiple_alignment.hh:65
bool has_stacking_
whether stacking probabilities are available
Definition: rna_data_impl.hh:52