1 #ifndef __VIENNA_RNA_PACKAGE_SNOOP_H__
2 #define __VIENNA_RNA_PACKAGE_SNOOP_H__
4 #include "data_structures.h"
6 *** computes snoRNA-RNA interactions in RNAduplex manner
9 snoopT snoopfold( const char *s1,
18 const int max_half_stem,
25 const int fullStemEnergy);
28 *** computes snoRNA-RNA suboptimal interactions in RNAduplex manner
32 snoopT *snoop_subopt( const char *s1,
46 const int max_half_stem,
53 const int fullStemEnergy);
56 *** computes snoRNA-RNA suboptimal interactions in a RNAplex manner
61 void Lsnoop_subopt( const char *s1,
75 const int max_half_stem,
82 const int alignment_length,
84 const int fullStemEnergy);
87 *** computes snoRNA-RNA suboptimal interactions in a RNAplex manner. The stem energy is saved into a list of struct, leading to a runtime improvement of 20%
92 void Lsnoop_subopt_list ( const char *s1,
106 const int max_half_stem,
113 const int alignment_length,
115 const int fullStemEnergy);
118 *** computes snoRNA-RNA suboptimal interactions in a RNAplex manner. The stem energy is saved into a list of struct, leading to a runtime improvement of 20%. It considers accessibility
122 void Lsnoop_subopt_list_XS (const char *s1,
124 const int **access_s1,
128 const int threshloop,
137 const int max_half_stem,
144 const int alignment_length,
146 const int fullStemEnergy);
150 *** computes snoRNA-RNA suboptimal interactions in a RNAduplex manner, and considers accessibility
154 void snoop_subopt_XS (const char *s1,
156 const int **access_s1,
160 const int threshloop,
169 const int max_half_stem,
176 const int alignment_length,
178 const int fullStemEnergy);
181 *** aliduplex-like alignment version of snoop_subopt
184 snoopT *alisnoop_subopt(const char **s1,
189 const int threshloop,
198 const int max_half_stem,
207 *** RNAplex-like Alignment version of snoop_subopt
212 snoopT *aliLsnoop_subopt_list ( const char **s1,
217 const int threshloop,
226 const int max_half_stem,
233 const int alignment_length);
235 *** RNAaliduplex-like version of snoopfold
239 snoopT alisnoopfold(const char **s1,
242 const int threshloop,
248 const int max_half_stem,
256 *** RNAduplex-like version of snoopfold with accessibility information
259 snoopT snoopfold_XS(const char *s1,
261 const int **access_s1,
265 const int threshloop,
271 const int max_half_stem,
278 const int fullStemEnergy);
283 extern int snoop_subopt_sorted;