binaries/src/ViennaRNA/H/ali_plex.h

   1 #ifndef __VIENNA_RNA_PACKAGE_ALI_PLEX_H__
   2 #define __VIENNA_RNA_PACKAGE_ALI_PLEX_H__
   3
   4 #include "data_structures.h"
   5 /**
   6 *** aliLduplexfold computes the duplexes between two alignments
   7 **/
   8 duplexT** aliLduplexfold( const char *s1[],
   9                           const char *s2[],
  10                           const int threshold,
  11                           const int extension_cost,
  12                           const int alignment_length,
  13                           const int delta,
  14                           const int fast,
  15                           const int il_a,
  16                           const int il_b,
  17                           const int b_a,
  18                           const int b_b);
  19 /**
  20 *** aliLduplexfold computes the duplexes between two alignments. It also takes the average accessibility into account
  21 **/
  22 duplexT** aliLduplexfold_XS(const char* s1[],
  23                             const char* s2[],
  24                             const int **access_s1,
  25                             const int **access_s2,
  26                             const int threshold,
  27                             const int alignment_length,
  28                             const int delta,
  29                             const int fast,
  30                             const int il_a,
  31                             const int il_b,
  32                             const int b_a,
  33                             const int b_b);
  34
  35 /*
  36 extern duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension_cost);
  37 extern duplexT aliduplexfold_XS(const char *s1[], const char *s2[],const int **access_s1,
  38 const int **access_s2, const int i_pos, const int j_pos, const int threshold);
  39 */
  40 #endif