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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