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# 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