RNAlib-2.0.5
H/plex.h
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