1 #ifndef __VIENNA_RNA_PACKAGE_PLEX_H__
2 #define __VIENNA_RNA_PACKAGE_PLEX_H__
4 #include "data_structures.h"
7 extern int subopt_sorted;
10 *** Lduplexfold Computes duplexes between two single sequences
12 duplexT** Lduplexfold(const char *s1,
15 const int extension_cost,
16 const int alignment_length,
25 *** Lduplexfold_XS Computes duplexes between two single sequences with accessibility
27 duplexT** Lduplexfold_XS( const char*s1,
29 const int **access_s1,
30 const int **access_s2,
33 const int alignment_length,
38 const int b_b);/* , const int target_dead, const int query_dead); */
41 *** Lduplexfold_C Computes duplexes between two single sequences and takes constraint into account
43 duplexT** Lduplexfold_C(const char *s1,
46 const int extension_cost,
47 const int alignment_length,
50 const char* structure,
57 *** Lduplexfold_CXS Computes duplexes between two single sequences and takes constraint as well as accessibility into account
60 duplexT** Lduplexfold_CXS(const char*s1,
62 const int **access_s1,
63 const int **access_s2,
66 const int alignment_length,
68 const char* structure,
72 const int b_b); /*, const int target_dead, const int query_dead); */
77 int arraySize(duplexT** array);
78 void freeDuplexT(duplexT** array);