1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H 2 #define VIENNA_RNA_PACKAGE_LPFOLD_H 44 #ifdef VRNA_WARN_DEPRECATED 46 # define DEPRECATED(func) func __attribute__ ((deprecated)) 48 # define DEPRECATED(func) func 51 # define DEPRECATED(func) func 55 #define VRNA_EXT_LOOP 1U 56 #define VRNA_HP_LOOP 2U 57 #define VRNA_INT_LOOP 4U 58 #define VRNA_MB_LOOP 8U 59 #define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP) 67 #define VRNA_PROBS_WINDOW_BPP 4096U 74 #define VRNA_PROBS_WINDOW_UP 8192U 81 #define VRNA_PROBS_WINDOW_STACKP 16384U 88 #define VRNA_PROBS_WINDOW_UP_SPLIT 32768U 91 #define VRNA_PROBS_WINDOW_PF 65536U 229 unsigned int options,
234 #ifdef VRNA_BACKWARD_COMPAT 243 DEPRECATED(
void update_pf_paramsLP(
int length));
252 DEPRECATED(
void update_pf_paramsLP_par(
int length,
293 DEPRECATED(
vrna_ep_t *pfl_fold(
char *sequence,
309 DEPRECATED(
vrna_ep_t *pfl_fold_par(
char *sequence,
320 DEPRECATED(
void putoutpU_prob_par(
double **pU,
342 DEPRECATED(
void putoutpU_prob(
double **pU,
349 DEPRECATED(
void putoutpU_prob_bin_par(
double **pU,
371 DEPRECATED(
void putoutpU_prob_bin(
double **pU,
383 DEPRECATED(
void init_pf_foldLP(
int length));
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structure_utils.h:69
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
void vrna_pfl_fold_up_cb(const char *sequence, int ulength, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data)
Compute probability of contiguous unpaired segments.
vrna_ep_t * vrna_pfl_fold(const char *sequence, int window_size, int max_bp_span, float cutoff)
Compute base pair probabilities using a sliding-window approach.
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
void( vrna_probs_window_callback)(FLT_OR_DBL *pr, int pr_size, int i, int max, unsigned int type, void *data)
Sliding window probability computation callback.
Definition: LPfold.h:34
void vrna_pfl_fold_cb(const char *sequence, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data)
Compute base pair probabilities using a sliding-window approach (callback version) ...
double ** vrna_pfl_fold_up(const char *sequence, int ulength, int window_size, int max_bp_span)
Compute probability of contiguous unpaired segments.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
int max_bp_span
Maximum allowed base pair span.
void vrna_probs_window(vrna_fold_compound_t *fc, int ulength, unsigned int options, vrna_probs_window_callback *cb, void *data)
Compute various equilibrium probabilities under a sliding window approach.