RNAlib-2.4.3
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Partition function implementation for the Lfold algorithm. More...
Go to the source code of this file.
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... | |
Partition function implementation for the Lfold algorithm.
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.
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 |