binaries/src/ViennaRNA/H/plex.h

   1 #ifndef __VIENNA_RNA_PACKAGE_PLEX_H__
   2 #define __VIENNA_RNA_PACKAGE_PLEX_H__
   3
   4 #include "data_structures.h"
   5
   6
   7 extern int subopt_sorted;
   8
   9 /**
  10 *** Lduplexfold Computes duplexes between two single sequences
  11 **/
  12 duplexT** Lduplexfold(const char *s1,
  13                       const char *s2,
  14                       const int threshold,
  15                       const int extension_cost,
  16                       const int alignment_length,
  17                       const int delta,
  18                       const int fast,
  19                       const int il_a,
  20                       const int il_b,
  21                       const int b_a,
  22                       const int b_b);
  23
  24 /**
  25 *** Lduplexfold_XS Computes duplexes between two single sequences with accessibility
  26 **/
  27 duplexT** Lduplexfold_XS( const char*s1,
  28                           const char* s2,
  29                           const int **access_s1,
  30                           const int **access_s2,
  31                           const int threshold,
  32                           const int delta,
  33                           const int alignment_length,
  34                           const int fast,
  35                           const int il_a,
  36                           const int il_b,
  37                           const int b_a,
  38                           const int b_b);/* , const int target_dead, const int query_dead); */
  39
  40 /**
  41 *** Lduplexfold_C Computes duplexes between two single sequences and takes constraint into account
  42 **/
  43 duplexT** Lduplexfold_C(const char *s1,
  44                         const char *s2,
  45                         const int threshold,
  46                         const int extension_cost,
  47                         const int alignment_length,
  48                         const int delta,
  49                         const int fast,
  50                         const char* structure,
  51                         const int il_a,
  52                         const int il_b,
  53                         const int b_a,
  54                         const int b_b);
  55
  56 /**
  57 *** Lduplexfold_CXS Computes duplexes between two single sequences and takes constraint as well as accessibility into account
  58 **/
  59
  60 duplexT** Lduplexfold_CXS(const char*s1,
  61                           const char* s2,
  62                           const int **access_s1,
  63                           const int **access_s2,
  64                           const int threshold,
  65                           const int delta,
  66                           const int alignment_length,
  67                           const int fast,
  68                           const char* structure,
  69                           const int il_a,
  70                           const int il_b,
  71                           const int b_a,
  72                           const int b_b); /*, const int target_dead, const int query_dead); */
  73
  74
  75
  76
  77 int      arraySize(duplexT** array);
  78 void     freeDuplexT(duplexT** array);
  79
  80 #endif