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# 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