RNAlib-2.1.9
snoop.h
1 #ifndef __VIENNA_RNA_PACKAGE_SNOOP_H__
2 #define __VIENNA_RNA_PACKAGE_SNOOP_H__
3 
4 #include "data_structures.h"
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 
32 snoopT *snoop_subopt( const char *s1,
33  const char *s2,
34  int delta,
35  int w,
36  const int penalty,
37  const int threshloop,
38  const int threshLE,
39  const int threshRE,
40  const int threshDE,
41  const int threshTE,
42  const int threshSE,
43  const int threshD,
44  const int distance,
45  const int half_stem,
46  const int max_half_stem,
47  const int min_s2,
48  const int max_s2,
49  const int min_s1,
50  const int max_s1,
51  const int min_d1,
52  const int min_d2,
53  const int fullStemEnergy);
54 
61 void Lsnoop_subopt( const char *s1,
62  const char *s2,
63  int delta,
64  int w,
65  const int penalty,
66  const int threshloop,
67  const int threshLE,
68  const int threshRE,
69  const int threshDE,
70  const int threshTE,
71  const int threshSE,
72  const int threshD,
73  const int distance,
74  const int half_stem,
75  const int max_half_stem,
76  const int min_s2,
77  const int max_s2,
78  const int min_s1,
79  const int max_s1,
80  const int min_d1,
81  const int min_d2,
82  const int alignment_length,
83  const char* name,
84  const int fullStemEnergy);
85 
92 void Lsnoop_subopt_list ( const char *s1,
93  const char *s2,
94  int delta,
95  int w,
96  const int penalty,
97  const int threshloop,
98  const int threshLE,
99  const int threshRE,
100  const int threshDE,
101  const int threshTE,
102  const int threshSE,
103  const int threshD,
104  const int distance,
105  const int half_stem,
106  const int max_half_stem,
107  const int min_s2,
108  const int max_s2,
109  const int min_s1,
110  const int max_s1,
111  const int min_d1,
112  const int min_d2,
113  const int alignment_length,
114  const char *name,
115  const int fullStemEnergy);
116 
122 void Lsnoop_subopt_list_XS (const char *s1,
123  const char *s2,
124  const int **access_s1,
125  int delta,
126  int w,
127  const int penalty,
128  const int threshloop,
129  const int threshLE,
130  const int threshRE,
131  const int threshDE,
132  const int threshTE,
133  const int threshSE,
134  const int threshD,
135  const int distance,
136  const int half_stem,
137  const int max_half_stem,
138  const int min_s2,
139  const int max_s2,
140  const int min_s1,
141  const int max_s1,
142  const int min_d1,
143  const int min_d2,
144  const int alignment_length,
145  const char *name,
146  const int fullStemEnergy);
147 
148 
154 void snoop_subopt_XS (const char *s1,
155  const char *s2,
156  const int **access_s1,
157  int delta,
158  int w,
159  const int penalty,
160  const int threshloop,
161  const int threshLE,
162  const int threshRE,
163  const int threshDE,
164  const int threshTE,
165  const int threshSE,
166  const int threshD,
167  const int distance,
168  const int half_stem,
169  const int max_half_stem,
170  const int min_s2,
171  const int max_s2,
172  const int min_s1,
173  const int max_s1,
174  const int min_d1,
175  const int min_d2,
176  const int alignment_length,
177  const char *name,
178  const int fullStemEnergy);
179 
184 snoopT *alisnoop_subopt(const char **s1,
185  const char **s2,
186  int delta,
187  int w,
188  const int penalty,
189  const int threshloop,
190  const int threshLE,
191  const int threshRE,
192  const int threshDE,
193  const int threshTE,
194  const int threshSE,
195  const int threshD,
196  const int distance,
197  const int half_stem,
198  const int max_half_stem,
199  const int min_s2,
200  const int max_s2,
201  const int min_s1,
202  const int max_s1,
203  const int min_d1,
204  const int min_d2);
205 
212 snoopT *aliLsnoop_subopt_list ( const char **s1,
213  const char **s2,
214  int delta,
215  int w,
216  const int penalty,
217  const int threshloop,
218  const int threshLE,
219  const int threshRE,
220  const int threshDE,
221  const int threshTE,
222  const int threshSE,
223  const int threshD,
224  const int distance,
225  const int half_stem,
226  const int max_half_stem,
227  const int min_s2,
228  const int max_s2,
229  const int min_s1,
230  const int max_s1,
231  const int min_d1,
232  const int min_d2,
233  const int alignment_length);
239 snoopT alisnoopfold(const char **s1,
240  const char **s2,
241  const int penalty,
242  const int threshloop,
243  const int threshLE,
244  const int threshRE,
245  const int threshDE,
246  const int threshD,
247  const int half_stem,
248  const int max_half_stem,
249  const int min_s2,
250  const int max_s2,
251  const int min_s1,
252  const int max_s1,
253  const int min_d1,
254  const int min_d2);
259 snoopT snoopfold_XS(const char *s1,
260  const char *s2,
261  const int **access_s1,
262  const int pos,
263  const int max_pos_j,
264  const int penalty,
265  const int threshloop,
266  const int threshLE,
267  const int threshRE,
268  const int threshDE,
269  const int threshD,
270  const int half_stem,
271  const int max_half_stem,
272  const int min_s2,
273  const int max_s2,
274  const int min_s1,
275  const int max_s1,
276  const int min_d1,
277  const int min_d2,
278  const int fullStemEnergy);
279 
280 
281 
282 
283 extern int snoop_subopt_sorted;
284 #endif