RNAlib-2.0.1
|
00001 #ifndef __VIENNA_RNA_PACKAGE_PLEX_H__ 00002 #define __VIENNA_RNA_PACKAGE_PLEX_H__ 00003 00004 #include "data_structures.h" 00005 00006 00007 extern int subopt_sorted; 00008 00012 duplexT** Lduplexfold(const char *s1, 00013 const char *s2, 00014 const int threshold, 00015 const int extension_cost, 00016 const int alignment_length, 00017 const int delta, 00018 const int fast, 00019 const int il_a, 00020 const int il_b, 00021 const int b_a, 00022 const int b_b); 00023 00027 duplexT** Lduplexfold_XS( const char*s1, 00028 const char* s2, 00029 const int **access_s1, 00030 const int **access_s2, 00031 const int threshold, 00032 const int delta, 00033 const int alignment_length, 00034 const int fast, 00035 const int il_a, 00036 const int il_b, 00037 const int b_a, 00038 const int b_b);//, const int target_dead, const int query_dead); 00039 00043 duplexT** Lduplexfold_C(const char *s1, 00044 const char *s2, 00045 const int threshold, 00046 const int extension_cost, 00047 const int alignment_length, 00048 const int delta, 00049 const int fast, 00050 const char* structure, 00051 const int il_a, 00052 const int il_b, 00053 const int b_a, 00054 const int b_b); 00055 00060 duplexT** Lduplexfold_CXS(const char*s1, 00061 const char* s2, 00062 const int **access_s1, 00063 const int **access_s2, 00064 const int threshold, 00065 const int delta, 00066 const int alignment_length, 00067 const int fast, 00068 const char* structure, 00069 const int il_a, 00070 const int il_b, 00071 const int b_a, 00072 const int b_b);//, const int target_dead, const int query_dead); 00073 00074 00075 00076 00077 int arraySize(duplexT** array); 00078 void freeDuplexT(duplexT** array); 00079 00080 #endif