RNAlib-2.0.1
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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