RNAlib-2.0.6
H/ali_plex.h
00001 #ifndef __VIENNA_RNA_PACKAGE_ALI_PLEX_H__
00002 #define __VIENNA_RNA_PACKAGE_ALI_PLEX_H__
00003 
00004 #include "data_structures.h"
00008 duplexT** aliLduplexfold( const char *s1[],
00009                           const char *s2[],
00010                           const int threshold,
00011                           const int extension_cost,
00012                           const int alignment_length,
00013                           const int delta,
00014                           const int fast,
00015                           const int il_a,
00016                           const int il_b,
00017                           const int b_a,
00018                           const int b_b);
00022 duplexT** aliLduplexfold_XS(const char* s1[],
00023                             const char* s2[],
00024                             const int **access_s1,
00025                             const int **access_s2, 
00026                             const int threshold,
00027                             const int alignment_length,
00028                             const int delta,
00029                             const int fast,
00030                             const int il_a,
00031                             const int il_b,
00032                             const int b_a,
00033                             const int b_b);
00034 
00035 /*
00036 extern duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension_cost);
00037 extern duplexT aliduplexfold_XS(const char *s1[], const char *s2[],const int **access_s1, 
00038 const int **access_s2, const int i_pos, const int j_pos, const int threshold);
00039 */
00040 #endif