1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H 2 #define VIENNA_RNA_PACKAGE_LPFOLD_H 11 typedef void (vrna_probs_window_callback)(
FLT_OR_DBL *
pr,
21 #ifdef VRNA_WARN_DEPRECATED 23 # define DEPRECATED(func) func __attribute__ ((deprecated)) 25 # define DEPRECATED(func) func 28 # define DEPRECATED(func) func 32 #define VRNA_EXT_LOOP 1U 33 #define VRNA_HP_LOOP 2U 34 #define VRNA_INT_LOOP 4U 35 #define VRNA_MB_LOOP 8U 36 #define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP) 44 #define VRNA_PROBS_WINDOW_BPP 4096U 51 #define VRNA_PROBS_WINDOW_UP 8192U 58 #define VRNA_PROBS_WINDOW_STACKP 16384U 65 #define VRNA_PROBS_WINDOW_UP_SPLIT 32768U 120 vrna_probs_window_callback *cb,
183 vrna_probs_window_callback *cb,
203 vrna_probs_window_callback *cb,
205 unsigned int options);
208 #ifdef VRNA_BACKWARD_COMPAT 217 DEPRECATED(
void update_pf_paramsLP(
int length));
226 DEPRECATED(
void update_pf_paramsLP_par(
int length,
294 DEPRECATED(
void putoutpU_prob_par(
double **pU,
316 DEPRECATED(
void putoutpU_prob(
double **pU,
323 DEPRECATED(
void putoutpU_prob_bin_par(
double **pU,
345 DEPRECATED(
void putoutpU_prob_bin(
double **pU,
357 DEPRECATED(
void init_pf_foldLP(
int length));
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:457
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.
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:99
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) ...
double ** vrna_pfl_fold_up(const char *sequence, int ulength, int window_size, int max_bp_span)
Compute probability of contiguous unpaired segments.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:183
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
int max_bp_span
Maximum allowed base pair span.
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.
vrna_plist_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.