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

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

diff --git a/binaries/src/ViennaRNA/H/profiledist.h b/binaries/src/ViennaRNA/H/profiledist.h
new file mode 100644 (file)
index 0000000..847f2bb
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+++ b/binaries/src/ViennaRNA/H/profiledist.h
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+#ifndef __VIENNA_RNA_PACKAGE_PROFILEDIST_H__
+#define __VIENNA_RNA_PACKAGE_PROFILEDIST_H__
+
+#ifdef __GNUC__
+#define DEPRECATED(func) func __attribute__ ((deprecated))
+#else
+#define DEPRECATED(func) func
+#endif
+
+#include "data_structures.h"
+
+/** \file profiledist.h  */
+
+/**
+ *  \brief Align the 2 probability profiles T1, T2\n
+ * 
+ *  This is like a Needleman-Wunsch alignment,
+ *  we should really use affine gap-costs ala Gotoh
+ */
+float profile_edit_distance(const float *T1,
+                            const float *T2);
+
+/**
+ *  \brief condense pair probability matrix into a vector containing probabilities
+ *  for unpaired, upstream paired and downstream paired.
+ * 
+ *  This resulting probability profile is used as input for profile_edit_distance
+ * 
+ *  \param bppm   A pointer to the base pair probability matrix
+ *  \param length The length of the sequence
+ *  \returns      The bp profile
+ */
+float *Make_bp_profile_bppm(FLT_OR_DBL *bppm,
+                            int length);
+
+/**
+ *  \brief print string representation of probability profile
+ */
+void  print_bppm(const float *T);
+
+/**
+ *  \brief free space allocated in Make_bp_profile
+ * 
+ *  Backward compatibility only. You can just use plain free()
+ */
+void  free_profile(float *T);
+
+/**
+ *  \note This function is NOT threadsafe
+ * 
+ *  \see Make_bp_profile_bppm()
+ * 
+ *  \deprecated This function is deprecated and will be removed soon! See \ref Make_bp_profile_bppm() for a replacement
+ * 
+ */
+DEPRECATED(float *Make_bp_profile(int length));
+
+#endif