RNAlib-2.4.10
snoop.h
1 #ifndef VIENNA_RNA_PACKAGE_SNOOP_H
2 #define VIENNA_RNA_PACKAGE_SNOOP_H
3 
9 snoopT snoopfold(const char *s1,
10  const char *s2,
11  const int penalty,
12  const int threshloop,
13  const int threshLE,
14  const int threshRE,
15  const int threshDE,
16  const int threshD,
17  const int half_stem,
18  const int max_half_stem,
19  const int min_s2,
20  const int max_s2,
21  const int min_s1,
22  const int max_s1,
23  const int min_d1,
24  const int min_d2,
25  const int fullStemEnergy);
26 
27 
33 snoopT *snoop_subopt(const char *s1,
34  const char *s2,
35  int delta,
36  int w,
37  const int penalty,
38  const int threshloop,
39  const int threshLE,
40  const int threshRE,
41  const int threshDE,
42  const int threshTE,
43  const int threshSE,
44  const int threshD,
45  const int distance,
46  const int half_stem,
47  const int max_half_stem,
48  const int min_s2,
49  const int max_s2,
50  const int min_s1,
51  const int max_s1,
52  const int min_d1,
53  const int min_d2,
54  const int fullStemEnergy);
55 
56 
62 void Lsnoop_subopt(const char *s1,
63  const char *s2,
64  int delta,
65  int w,
66  const int penalty,
67  const int threshloop,
68  const int threshLE,
69  const int threshRE,
70  const int threshDE,
71  const int threshTE,
72  const int threshSE,
73  const int threshD,
74  const int distance,
75  const int half_stem,
76  const int max_half_stem,
77  const int min_s2,
78  const int max_s2,
79  const int min_s1,
80  const int max_s1,
81  const int min_d1,
82  const int min_d2,
83  const int alignment_length,
84  const char *name,
85  const int fullStemEnergy);
86 
87 
93 void Lsnoop_subopt_list(const char *s1,
94  const char *s2,
95  int delta,
96  int w,
97  const int penalty,
98  const int threshloop,
99  const int threshLE,
100  const int threshRE,
101  const int threshDE,
102  const int threshTE,
103  const int threshSE,
104  const int threshD,
105  const int distance,
106  const int half_stem,
107  const int max_half_stem,
108  const int min_s2,
109  const int max_s2,
110  const int min_s1,
111  const int max_s1,
112  const int min_d1,
113  const int min_d2,
114  const int alignment_length,
115  const char *name,
116  const int fullStemEnergy);
117 
118 
124 void Lsnoop_subopt_list_XS(const char *s1,
125  const char *s2,
126  const int **access_s1,
127  int delta,
128  int w,
129  const int penalty,
130  const int threshloop,
131  const int threshLE,
132  const int threshRE,
133  const int threshDE,
134  const int threshTE,
135  const int threshSE,
136  const int threshD,
137  const int distance,
138  const int half_stem,
139  const int max_half_stem,
140  const int min_s2,
141  const int max_s2,
142  const int min_s1,
143  const int max_s1,
144  const int min_d1,
145  const int min_d2,
146  const int alignment_length,
147  const char *name,
148  const int fullStemEnergy);
149 
150 
156 void snoop_subopt_XS(const char *s1,
157  const char *s2,
158  const int **access_s1,
159  int delta,
160  int w,
161  const int penalty,
162  const int threshloop,
163  const int threshLE,
164  const int threshRE,
165  const int threshDE,
166  const int threshTE,
167  const int threshSE,
168  const int threshD,
169  const int distance,
170  const int half_stem,
171  const int max_half_stem,
172  const int min_s2,
173  const int max_s2,
174  const int min_s1,
175  const int max_s1,
176  const int min_d1,
177  const int min_d2,
178  const int alignment_length,
179  const char *name,
180  const int fullStemEnergy);
181 
182 
187 snoopT *alisnoop_subopt(const char **s1,
188  const char **s2,
189  int delta,
190  int w,
191  const int penalty,
192  const int threshloop,
193  const int threshLE,
194  const int threshRE,
195  const int threshDE,
196  const int threshTE,
197  const int threshSE,
198  const int threshD,
199  const int distance,
200  const int half_stem,
201  const int max_half_stem,
202  const int min_s2,
203  const int max_s2,
204  const int min_s1,
205  const int max_s1,
206  const int min_d1,
207  const int min_d2);
208 
209 
215 snoopT *aliLsnoop_subopt_list(const char **s1,
216  const char **s2,
217  int delta,
218  int w,
219  const int penalty,
220  const int threshloop,
221  const int threshLE,
222  const int threshRE,
223  const int threshDE,
224  const int threshTE,
225  const int threshSE,
226  const int threshD,
227  const int distance,
228  const int half_stem,
229  const int max_half_stem,
230  const int min_s2,
231  const int max_s2,
232  const int min_s1,
233  const int max_s1,
234  const int min_d1,
235  const int min_d2,
236  const int alignment_length);
237 
238 
244 snoopT alisnoopfold(const char **s1,
245  const char **s2,
246  const int penalty,
247  const int threshloop,
248  const int threshLE,
249  const int threshRE,
250  const int threshDE,
251  const int threshD,
252  const int half_stem,
253  const int max_half_stem,
254  const int min_s2,
255  const int max_s2,
256  const int min_s1,
257  const int max_s1,
258  const int min_d1,
259  const int min_d2);
260 
261 
266 snoopT snoopfold_XS(const char *s1,
267  const char *s2,
268  const int **access_s1,
269  const int pos,
270  const int max_pos_j,
271  const int penalty,
272  const int threshloop,
273  const int threshLE,
274  const int threshRE,
275  const int threshDE,
276  const int threshD,
277  const int half_stem,
278  const int max_half_stem,
279  const int min_s2,
280  const int max_s2,
281  const int min_s1,
282  const int max_s1,
283  const int min_d1,
284  const int min_d2,
285  const int fullStemEnergy);
286 
287 
288 extern int snoop_subopt_sorted;
289 #endif
Data structure for RNAsnoop.
Definition: basic.h:248
Various data structures and pre-processor macros.