binaries/src/ViennaRNA/H/snofold.h

   1 /* function from fold.c */
   2 #ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__
   3 #define __VIENNA_RNA_PACKAGE_SNOFOLD_H__
   4
   5 #include "data_structures.h"
   6
   7 /* Normal fold */
   8
   9 /**
  10 *** snofold is the stem folding array for RNAsnoop
  11 **/
  12 int  snofold( const char *sequence,
  13                 char *structure,
  14                 const int max_assym,
  15                 const int threshold,
  16                 const int min_s2,
  17                 const int max_s2,
  18                 const int half_stem,
  19                 const int max_half_stem);
  20 /**
  21 *** Free arrays and structure related to snofold
  22 **/
  23
  24 void   snofree_arrays(const int length);  /* free arrays for mfe folding */
  25 void   snoinitialize_fold(int length);    /* allocate arrays for folding */
  26 void   snoupdate_fold_params(void);       /* recalculate parameters */
  27 int    snoloop_energy(short *ptable,
  28                       short *s,
  29                       short *s1,
  30                       int i);
  31 void   snoexport_fold_arrays( int **indx_p,
  32                               int **mLoop_p,
  33                               int **cLoop,
  34                               folden ***fold_p,
  35                               folden ***fold_p_XS);
  36 char * snobacktrack_fold_from_pair( const char *sequence,
  37                                     int i,
  38                                     int j);
  39 /* alifold */
  40 float alisnofold( const char **strings,
  41                   const int max_assym,
  42                   const int threshloop,
  43                   const int min_s2,
  44                   const int max_s2,
  45                   const int half_stem,
  46                   const int max_half_stem);
  47 void  alisnofree_arrays(const int length);
  48 char  *alisnobacktrack_fold_from_pair(const char **sequence,
  49                                       int i,
  50                                       int j,
  51                                       int *cov);
  52 extern double cv_fact /* =1 */;
  53 extern double nc_fact /* =1 */;
  54
  55 /* max number of mismatch >>>>>..((   )).>>>> */
  56 #define MISMATCH 3
  57
  58 #endif