RNAlib-2.4.3
LPfold.h File Reference

Partition function implementation for the Lfold algorithm. More...

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Macros

#define VRNA_PROBS_WINDOW_BPP   4096U
 Option flag to activate callback triggers for pairing probabilities. More...
 
#define VRNA_PROBS_WINDOW_UP   8192U
 Option flag to activate callback triggers for unpaired probabilities. More...
 
#define VRNA_PROBS_WINDOW_STACKP   16384U
 Option flag to activate callback triggers for stacking probabilities. More...
 
#define VRNA_PROBS_WINDOW_UP_SPLIT   32768U
 Option flag to activate callback triggers for unpaired probabilities (split up into different loop types) More...
 

Typedefs

typedef 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. More...
 

Functions

vrna_ep_tvrna_pfl_fold (const char *sequence, int window_size, int max_bp_span, float cutoff)
 Compute base pair probabilities using a sliding-window approach. More...
 
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) More...
 
double ** vrna_pfl_fold_up (const char *sequence, int ulength, int window_size, int max_bp_span)
 Compute probability of contiguous unpaired segments. More...
 
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. More...
 
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. More...
 

Detailed Description

Partition function implementation for the Lfold algorithm.

Typedef Documentation

◆ vrna_probs_window_callback

typedef 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.

Notes on Callback Functions:
This function will be called for each probability data set in the sliding window probability computation implementation of vrna_probs_window(). The argument type specifies the type of probability that is passed to this function.
See also
vrna_probs_window(), vrna_pfl_fold_up_cb() VRNA_PROBS_WINDOW_BPP, VRNA_PROBS_WINDOW_UP, VRNA_PROBS_WINDOW_STACKP, #VRNA_EXT_LOOP, #VRNA_HP_LOOP, #VRNA_INT_LOOP, #VRNA_MB_LOOP, #VRNA_ANY_LOOP
Parameters
prAn array of probabilities
pr_sizeThe length of the probability array
iThe i-position (5') of the probabilities
maxThe (theoretical) maximum length of the probability array
dataAuxiliary data