X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2FViennaRNA%2FH%2Fplex.h;fp=binaries%2Fsrc%2FViennaRNA%2FH%2Fplex.h;h=d33cef30bddc0274c965a57baea68536a8ff5a40;hb=7522ace91fc0804a9719dbac9f68bc8154da3132;hp=0000000000000000000000000000000000000000;hpb=8116c0444fe98e8eb21bcdd8ded06e1429085823;p=jabaws.git diff --git a/binaries/src/ViennaRNA/H/plex.h b/binaries/src/ViennaRNA/H/plex.h new file mode 100644 index 0000000..d33cef3 --- /dev/null +++ b/binaries/src/ViennaRNA/H/plex.h @@ -0,0 +1,80 @@ +#ifndef __VIENNA_RNA_PACKAGE_PLEX_H__ +#define __VIENNA_RNA_PACKAGE_PLEX_H__ + +#include "data_structures.h" + + +extern int subopt_sorted; + +/** +*** Lduplexfold Computes duplexes between two single sequences +**/ +duplexT** Lduplexfold(const char *s1, + const char *s2, + const int threshold, + const int extension_cost, + const int alignment_length, + const int delta, + const int fast, + const int il_a, + const int il_b, + const int b_a, + const int b_b); + +/** +*** Lduplexfold_XS Computes duplexes between two single sequences with accessibility +**/ +duplexT** Lduplexfold_XS( const char*s1, + const char* s2, + const int **access_s1, + const int **access_s2, + const int threshold, + const int delta, + const int alignment_length, + const int fast, + const int il_a, + const int il_b, + const int b_a, + const int b_b);/* , const int target_dead, const int query_dead); */ + +/** +*** Lduplexfold_C Computes duplexes between two single sequences and takes constraint into account +**/ +duplexT** Lduplexfold_C(const char *s1, + const char *s2, + const int threshold, + const int extension_cost, + const int alignment_length, + const int delta, + const int fast, + const char* structure, + const int il_a, + const int il_b, + const int b_a, + const int b_b); + +/** +*** Lduplexfold_CXS Computes duplexes between two single sequences and takes constraint as well as accessibility into account +**/ + +duplexT** Lduplexfold_CXS(const char*s1, + const char* s2, + const int **access_s1, + const int **access_s2, + const int threshold, + const int delta, + const int alignment_length, + const int fast, + const char* structure, + const int il_a, + const int il_b, + const int b_a, + const int b_b); /*, const int target_dead, const int query_dead); */ + + + + +int arraySize(duplexT** array); +void freeDuplexT(duplexT** array); + +#endif