part_func_window.h

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#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
#define VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H

#include <ViennaRNA/datastructures/basic.h>

typedef void (vrna_probs_window_callback)(FLT_OR_DBL    *pr,
                                          int           pr_size,
                                          int           i,
                                          int           max,
                                          unsigned int  type,
                                          void          *data);

#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/utils/structures.h>

#define VRNA_EXT_LOOP   1U

#define VRNA_HP_LOOP    2U

#define VRNA_INT_LOOP   4U

#define VRNA_MB_LOOP    8U

#define VRNA_ANY_LOOP   (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)


#define VRNA_PROBS_WINDOW_BPP  4096U

#define VRNA_PROBS_WINDOW_UP   8192U

#define VRNA_PROBS_WINDOW_STACKP   16384U

#define VRNA_PROBS_WINDOW_UP_SPLIT   32768U


#define VRNA_PROBS_WINDOW_PF        65536U

int
vrna_probs_window(vrna_fold_compound_t        *fc,
                  int                         ulength,
                  unsigned int                options,
                  vrna_probs_window_callback  *cb,
                  void                        *data);

/* End basic interface */
vrna_ep_t *
vrna_pfl_fold(const char  *sequence,
              int         window_size,
              int         max_bp_span,
              float       cutoff);


int
vrna_pfl_fold_cb(const char                 *sequence,
                 int                        window_size,
                 int                        max_bp_span,
                 vrna_probs_window_callback *cb,
                 void                       *data);


double **
vrna_pfl_fold_up(const char *sequence,
                 int        ulength,
                 int        window_size,
                 int        max_bp_span);


int
vrna_pfl_fold_up_cb(const char                  *sequence,
                    int                         ulength,
                    int                         window_size,
                    int                         max_bp_span,
                    vrna_probs_window_callback  *cb,
                    void                        *data);


/* End simplified interface */
#endif