- Main Page
- Related Pages
- Modules
- Data Structures
- Files

- File List
- Globals

# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snofold.h

    00001 /* function from fold.c */
    00002 #ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__
    00003 #define __VIENNA_RNA_PACKAGE_SNOFOLD_H__
    00004
    00005 #include "data_structures.h"
    00006
    00007 /* Normal fold */
    00008
    00012 int  snofold( const char *sequence,
    00013     char *structure,
    00014                 const int max_assym,
    00015                 const int threshold,
    00016                 const int min_s2,
    00017                 const int max_s2,
    00018                 const int half_stem,
    00019                 const int max_half_stem);
    00024 void   snofree_arrays(const int length);  /* free arrays for mfe folding */
    00025 void   snoinitialize_fold(int length);    /* allocate arrays for folding */
    00026 void   snoupdate_fold_params(void);       /* recalculate parameters */
    00027 int    snoloop_energy(short *ptable,
    00028                       short *s,
    00029                       short *s1,
    00030                       int i);
    00031 void   snoexport_fold_arrays( int **indx_p,
    00032                               int **mLoop_p,
    00033                               int **cLoop,
    00034                               folden ***fold_p,
    00035                               folden ***fold_p_XS);
    00036 char * snobacktrack_fold_from_pair( const char *sequence,
    00037                                     int i,
    00038                                     int j);
    00039 /* alifold */
    00040 float alisnofold( const char **strings,
    00041                   const int max_assym,
    00042                   const int threshloop,
    00043                   const int min_s2,
    00044                   const int max_s2,
    00045                   const int half_stem,
    00046                   const int max_half_stem);
    00047 void  alisnofree_arrays(const int length);
    00048 char  *alisnobacktrack_fold_from_pair(const char **sequence,
    00049                                       int i,
    00050                                       int j,
    00051                                       int *cov);
    00052 extern double cv_fact /* =1 */;
    00053 extern double nc_fact /* =1 */;
    00054
    00055 /* max number of mismatch >>>>>..((   )).>>>> */
    00056 #define MISMATCH 3
    00057
    00058 #endif