RNAlib-2.4.17
snoop.h
1 #ifndef VIENNA_RNA_PACKAGE_SNOOP_H
2 #define VIENNA_RNA_PACKAGE_SNOOP_H
3 
5 
6 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
7 
12 snoopT snoopfold(const char *s1,
13  const char *s2,
14  const int penalty,
15  const int threshloop,
16  const int threshLE,
17  const int threshRE,
18  const int threshDE,
19  const int threshD,
20  const int half_stem,
21  const int max_half_stem,
22  const int min_s2,
23  const int max_s2,
24  const int min_s1,
25  const int max_s1,
26  const int min_d1,
27  const int min_d2,
28  const int fullStemEnergy);
29 
30 
36 snoopT *snoop_subopt(const char *s1,
37  const char *s2,
38  int delta,
39  int w,
40  const int penalty,
41  const int threshloop,
42  const int threshLE,
43  const int threshRE,
44  const int threshDE,
45  const int threshTE,
46  const int threshSE,
47  const int threshD,
48  const int distance,
49  const int half_stem,
50  const int max_half_stem,
51  const int min_s2,
52  const int max_s2,
53  const int min_s1,
54  const int max_s1,
55  const int min_d1,
56  const int min_d2,
57  const int fullStemEnergy);
58 
59 
65 void Lsnoop_subopt(const char *s1,
66  const char *s2,
67  int delta,
68  int w,
69  const int penalty,
70  const int threshloop,
71  const int threshLE,
72  const int threshRE,
73  const int threshDE,
74  const int threshTE,
75  const int threshSE,
76  const int threshD,
77  const int distance,
78  const int half_stem,
79  const int max_half_stem,
80  const int min_s2,
81  const int max_s2,
82  const int min_s1,
83  const int max_s1,
84  const int min_d1,
85  const int min_d2,
86  const int alignment_length,
87  const char *name,
88  const int fullStemEnergy);
89 
90 
96 void Lsnoop_subopt_list(const char *s1,
97  const char *s2,
98  int delta,
99  int w,
100  const int penalty,
101  const int threshloop,
102  const int threshLE,
103  const int threshRE,
104  const int threshDE,
105  const int threshTE,
106  const int threshSE,
107  const int threshD,
108  const int distance,
109  const int half_stem,
110  const int max_half_stem,
111  const int min_s2,
112  const int max_s2,
113  const int min_s1,
114  const int max_s1,
115  const int min_d1,
116  const int min_d2,
117  const int alignment_length,
118  const char *name,
119  const int fullStemEnergy);
120 
121 
127 void Lsnoop_subopt_list_XS(const char *s1,
128  const char *s2,
129  const int **access_s1,
130  int delta,
131  int w,
132  const int penalty,
133  const int threshloop,
134  const int threshLE,
135  const int threshRE,
136  const int threshDE,
137  const int threshTE,
138  const int threshSE,
139  const int threshD,
140  const int distance,
141  const int half_stem,
142  const int max_half_stem,
143  const int min_s2,
144  const int max_s2,
145  const int min_s1,
146  const int max_s1,
147  const int min_d1,
148  const int min_d2,
149  const int alignment_length,
150  const char *name,
151  const int fullStemEnergy);
152 
153 
159 void snoop_subopt_XS(const char *s1,
160  const char *s2,
161  const int **access_s1,
162  int delta,
163  int w,
164  const int penalty,
165  const int threshloop,
166  const int threshLE,
167  const int threshRE,
168  const int threshDE,
169  const int threshTE,
170  const int threshSE,
171  const int threshD,
172  const int distance,
173  const int half_stem,
174  const int max_half_stem,
175  const int min_s2,
176  const int max_s2,
177  const int min_s1,
178  const int max_s1,
179  const int min_d1,
180  const int min_d2,
181  const int alignment_length,
182  const char *name,
183  const int fullStemEnergy);
184 
185 
190 snoopT *alisnoop_subopt(const char **s1,
191  const char **s2,
192  int delta,
193  int w,
194  const int penalty,
195  const int threshloop,
196  const int threshLE,
197  const int threshRE,
198  const int threshDE,
199  const int threshTE,
200  const int threshSE,
201  const int threshD,
202  const int distance,
203  const int half_stem,
204  const int max_half_stem,
205  const int min_s2,
206  const int max_s2,
207  const int min_s1,
208  const int max_s1,
209  const int min_d1,
210  const int min_d2);
211 
212 
218 snoopT *aliLsnoop_subopt_list(const char **s1,
219  const char **s2,
220  int delta,
221  int w,
222  const int penalty,
223  const int threshloop,
224  const int threshLE,
225  const int threshRE,
226  const int threshDE,
227  const int threshTE,
228  const int threshSE,
229  const int threshD,
230  const int distance,
231  const int half_stem,
232  const int max_half_stem,
233  const int min_s2,
234  const int max_s2,
235  const int min_s1,
236  const int max_s1,
237  const int min_d1,
238  const int min_d2,
239  const int alignment_length);
240 
241 
247 snoopT alisnoopfold(const char **s1,
248  const char **s2,
249  const int penalty,
250  const int threshloop,
251  const int threshLE,
252  const int threshRE,
253  const int threshDE,
254  const int threshD,
255  const int half_stem,
256  const int max_half_stem,
257  const int min_s2,
258  const int max_s2,
259  const int min_s1,
260  const int max_s1,
261  const int min_d1,
262  const int min_d2);
263 
264 
269 snoopT snoopfold_XS(const char *s1,
270  const char *s2,
271  const int **access_s1,
272  const int pos,
273  const int max_pos_j,
274  const int penalty,
275  const int threshloop,
276  const int threshLE,
277  const int threshRE,
278  const int threshDE,
279  const int threshD,
280  const int half_stem,
281  const int max_half_stem,
282  const int min_s2,
283  const int max_s2,
284  const int min_s1,
285  const int max_s1,
286  const int min_d1,
287  const int min_d2,
288  const int fullStemEnergy);
289 
290 
291 extern int snoop_subopt_sorted;
292 #endif
293 
294 #endif
snoopT
Data structure for RNAsnoop.
Definition: basic.h:248
basic.h
Various data structures and pre-processor macros.