1#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
2#define VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(DEPRECATED)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10# elif defined(__GNUC__)
11# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
13# define DEPRECATED(func, msg) func
16# define DEPRECATED(func, msg) func
85DEPRECATED(
typedef void (vrna_probs_window_callback)(
FLT_OR_DBL *
pr,
91 "Use vrna_probs_window_f instead!");
100#define VRNA_EXT_LOOP 1U
105#define VRNA_HP_LOOP 2U
110#define VRNA_INT_LOOP 4U
115#define VRNA_MB_LOOP 8U
120#define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)
135#define VRNA_PROBS_WINDOW_BPP 4096U
149#define VRNA_PROBS_WINDOW_UP 8192U
163#define VRNA_PROBS_WINDOW_STACKP 16384U
182#define VRNA_PROBS_WINDOW_UP_SPLIT 32768U
198#define VRNA_PROBS_WINDOW_PF 65536U
234 unsigned int options,
Various data structures and pre-processor macros.
The Basic Fold Compound API.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition basic.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
int max_bp_span
Maximum allowed base pair span.
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_up_cb(const char *sequence, int ulength, int window_size, int max_bp_span, vrna_probs_window_f cb, void *data)
Compute probability of contiguous unpaired segments.
int vrna_pfl_fold_cb(const char *sequence, int window_size, int max_bp_span, vrna_probs_window_f cb, void *data)
Compute base pair probabilities using a sliding-window approach (callback version)
void(* vrna_probs_window_f)(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:78
int vrna_probs_window(vrna_fold_compound_t *fc, int ulength, unsigned int options, vrna_probs_window_f cb, void *data)
Compute various equilibrium probabilities under a sliding window approach.
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:486
Various utility- and helper-functions for secondary structure parsing, converting,...