RNAlib-2.3.5
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...
 

Functions

vrna_plist_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, vrna_probs_window_callback *cb, void *data, unsigned int options)
 Compute various equilibrium probabilities under a sliding window approach. More...
 

Detailed Description

Partition function implementation for the Lfold algorithm.