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

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

diff --git a/binaries/src/ViennaRNA/H/ali_plex.h b/binaries/src/ViennaRNA/H/ali_plex.h
new file mode 100644 (file)
index 0000000..ab9a6c7
--- /dev/null
+++ b/binaries/src/ViennaRNA/H/ali_plex.h
@@ -0,0 +1,40 @@
+#ifndef __VIENNA_RNA_PACKAGE_ALI_PLEX_H__
+#define __VIENNA_RNA_PACKAGE_ALI_PLEX_H__
+
+#include "data_structures.h"
+/**
+*** aliLduplexfold computes the duplexes between two alignments
+**/
+duplexT** aliLduplexfold( 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);
+/**
+*** aliLduplexfold computes the duplexes between two alignments. It also takes the average accessibility into account
+**/
+duplexT** aliLduplexfold_XS(const char* s1[],
+                            const char* s2[],
+                            const int **access_s1,
+                            const int **access_s2, 
+                            const int threshold,
+                            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);
+
+/*
+extern duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension_cost);
+extern duplexT aliduplexfold_XS(const char *s1[], const char *s2[],const int **access_s1, 
+const int **access_s2, const int i_pos, const int j_pos, const int threshold);
+*/
+#endif