#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 upstream paired, downstream paired and unpaired.
 * 
 *  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