multibranch.h

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#ifndef VIENNA_RNA_PACKAGE_LOOPS_MULTIBRANCH_H
#define VIENNA_RNA_PACKAGE_LOOPS_MULTIBRANCH_H

#include <ViennaRNA/utils/basic.h>
#include <ViennaRNA/datastructures/basic.h>
#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/params/basic.h>

#ifdef VRNA_WARN_DEPRECATED
# if defined(DEPRECATED)
#   undef DEPRECATED
# endif
# if defined(__clang__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
# elif defined(__GNUC__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
# else
#  define DEPRECATED(func, msg) func
# endif
#else
# define DEPRECATED(func, msg) func
#endif

#ifdef __GNUC__
# define INLINE inline
#else
# define INLINE
#endif

int
vrna_E_mb_loop_stack(vrna_fold_compound_t *fc,
                     int                  i,
                     int                  j);


int
vrna_E_mb_loop_fast(vrna_fold_compound_t  *fc,
                    int                   i,
                    int                   j,
                    int                   *dmli1,
                    int                   *dmli2);


int
E_ml_rightmost_stem(int                   i,
                    int                   j,
                    vrna_fold_compound_t  *fc);


int
vrna_E_ml_stems_fast(vrna_fold_compound_t *fc,
                     int                  i,
                     int                  j,
                     int                  *fmi,
                     int                  *dmli);


/* End basic interface */
typedef struct vrna_mx_pf_aux_ml_s *vrna_mx_pf_aux_ml_t;


FLT_OR_DBL
vrna_exp_E_mb_loop_fast(vrna_fold_compound_t  *fc,
                        int                   i,
                        int                   j,
                        vrna_mx_pf_aux_ml_t   aux_mx);


vrna_mx_pf_aux_ml_t
vrna_exp_E_ml_fast_init(vrna_fold_compound_t *fc);


void
vrna_exp_E_ml_fast_rotate(vrna_mx_pf_aux_ml_t aux_mx);


void
vrna_exp_E_ml_fast_free(vrna_mx_pf_aux_ml_t aux_mx);


const FLT_OR_DBL *
vrna_exp_E_ml_fast_qqm(struct vrna_mx_pf_aux_ml_s *aux_mx);


const FLT_OR_DBL *
vrna_exp_E_ml_fast_qqm1(struct vrna_mx_pf_aux_ml_s *aux_mx);


FLT_OR_DBL
vrna_exp_E_ml_fast(vrna_fold_compound_t *fc,
                   int                  i,
                   int                  j,
                   vrna_mx_pf_aux_ml_t  aux_mx);


/* End partition function interface */
int
vrna_BT_mb_loop(vrna_fold_compound_t  *fc,
                int                   *i,
                int                   *j,
                int                   *k,
                int                   en,
                int                   *component1,
                int                   *component2);


int
vrna_BT_mb_loop_fake(vrna_fold_compound_t *fc,
                     int                  *u,
                     int                  *i,
                     int                  *j,
                     vrna_bp_stack_t      *bp_stack,
                     int                  *stack_count);


int
vrna_BT_mb_loop_split(vrna_fold_compound_t  *fc,
                      int                   *i,
                      int                   *j,
                      int                   *k,
                      int                   *l,
                      int                   *component1,
                      int                   *component2,
                      vrna_bp_stack_t       *bp_stack,
                      int                   *stack_count);


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

PRIVATE INLINE int
E_MLstem(int          type,
         int          si1,
         int          sj1,
         vrna_param_t *P)
{
  int energy = 0;

  if (si1 >= 0 && sj1 >= 0)
    energy += P->mismatchM[type][si1][sj1];
  else if (si1 >= 0)
    energy += P->dangle5[type][si1];
  else if (sj1 >= 0)
    energy += P->dangle3[type][sj1];

  if (type > 2)
    energy += P->TerminalAU;

  energy += P->MLintern[type];

  return energy;
}


PRIVATE INLINE FLT_OR_DBL
exp_E_MLstem(int              type,
             int              si1,
             int              sj1,
             vrna_exp_param_t *P)
{
  double energy = 1.0;

  if (si1 >= 0 && sj1 >= 0)
    energy = P->expmismatchM[type][si1][sj1];
  else if (si1 >= 0)
    energy = P->expdangle5[type][si1];
  else if (sj1 >= 0)
    energy = P->expdangle3[type][sj1];

  if (type > 2)
    energy *= P->expTermAU;

  energy *= P->expMLintern[type];
  return (FLT_OR_DBL)energy;
}


#endif

#endif