RNAlib-2.0.2
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 float  snofold( const char *sequence,
00013                 const int max_assym,
00014                 const int threshold, 
00015                 const int min_s2,
00016                 const int max_s2,
00017                 const int half_stem,
00018                 const int max_half_stem);
00023 void   snofree_arrays(const int length);           /* free arrays for mfe folding */
00024 void   snoinitialize_fold(int length); /* allocate arrays for folding */
00025 void   snoupdate_fold_params(void);    /* recalculate parameters */
00026 int    snoloop_energy(short *ptable,
00027                       short *s,
00028                       short *s1,
00029                       int i);
00030 void   snoexport_fold_arrays( int **indx_p,
00031                               int **mLoop_p,
00032                               int **cLoop,
00033                               folden ***fold_p,
00034                               folden ***fold_p_XS);
00035 char * snobacktrack_fold_from_pair( const char *sequence,
00036                                     int i,
00037                                     int j);
00038 //alifold
00039 float alisnofold( const char **strings,
00040                   const int max_assym,
00041                   const int threshloop, 
00042                   const int min_s2,
00043                   const int max_s2,
00044                   const int half_stem,
00045                   const int max_half_stem);
00046 void  alisnofree_arrays(const int length);
00047 char  *alisnobacktrack_fold_from_pair(const char **sequence,
00048                                       int i,
00049                                       int j,
00050                                       int *cov);
00051 extern double cv_fact /* =1 */;
00052 extern double nc_fact /* =1 */;
00053 //max number of mismatch >>>>>..((   )).>>>> 
00054 #define MISMATCH 3
00055 
00056 #endif