WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / H / plex.h

diff --git a/binaries/src/ViennaRNA/H/plex.h b/binaries/src/ViennaRNA/H/plex.h
new file mode 100644 (file)
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