Go to the documentation of this file. 1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
76 #define VRNA_EXT_LOOP 1U
81 #define VRNA_HP_LOOP 2U
86 #define VRNA_INT_LOOP 4U
91 #define VRNA_MB_LOOP 8U
96 #define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)
111 #define VRNA_PROBS_WINDOW_BPP 4096U
125 #define VRNA_PROBS_WINDOW_UP 8192U
139 #define VRNA_PROBS_WINDOW_STACKP 16384U
158 #define VRNA_PROBS_WINDOW_UP_SPLIT 32768U
174 #define VRNA_PROBS_WINDOW_PF 65536U
210 unsigned int options,
double ** vrna_pfl_fold_up(const char *sequence, int ulength, int window_size, int max_bp_span)
Compute probability of contiguous unpaired segments.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
int max_bp_span
Maximum allowed base pair span.
Various data structures and pre-processor macros.
int 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.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
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: part_func_window.h:63
int 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.
The Basic Fold Compound API.
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.
int 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)
Various utility- and helper-functions for secondary structure parsing, converting,...