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plex.h
1 #ifndef __VIENNA_RNA_PACKAGE_PLEX_H__
2 #define __VIENNA_RNA_PACKAGE_PLEX_H__
3
4 #include "data_structures.h"
5
6
7 extern int subopt_sorted;
8
12 duplexT** Lduplexfold(const char *s1,
13 const char *s2,
14 const int threshold,
15 const int extension_cost,
16 const int alignment_length,
17 const int delta,
18 const int fast,
19 const int il_a,
20 const int il_b,
21 const int b_a,
22 const int b_b);
23
27 duplexT** Lduplexfold_XS( const char*s1,
28 const char* s2,
29 const int **access_s1,
30 const int **access_s2,
31 const int threshold,
32 const int delta,
33 const int alignment_length,
34 const int fast,
35 const int il_a,
36 const int il_b,
37 const int b_a,
38 const int b_b);/* , const int target_dead, const int query_dead); */
39
43 duplexT** Lduplexfold_C(const char *s1,
44 const char *s2,
45 const int threshold,
46 const int extension_cost,
47 const int alignment_length,
48 const int delta,
49 const int fast,
50 const char* structure,
51 const int il_a,
52 const int il_b,
53 const int b_a,
54 const int b_b);
55
60 duplexT** Lduplexfold_CXS(const char*s1,
61 const char* s2,
62 const int **access_s1,
63 const int **access_s2,
64 const int threshold,
65 const int delta,
66 const int alignment_length,
67 const int fast,
68 const char* structure,
69 const int il_a,
70 const int il_b,
71 const int b_a,
72 const int b_b); /*, const int target_dead, const int query_dead); */
73
74
75
76
77 int arraySize(duplexT** array);
78 void freeDuplexT(duplexT** array);
79
80 #endif