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

Include dependency graph for LPfold.h:

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_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. 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

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

pr	An array of probabilities
pr_size	The length of the probability array
i	The i-position (5') of the probabilities
max	The (theoretical) maximum length of the probability array
data	Auxiliary data