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# 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