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1.6.1
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-snofold.h
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/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 +
1.6.1