/*
      minimum free energy
      RNA secondary structure with
      basepair distance d to reference structure prediction

*/
#ifndef __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__
#define __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__

/**
 *  \file 2Dfold.h
 *  \brief Compute the minimum free energy (MFE) and secondary structures for a partitioning of
 *  the secondary structure space according to the base pair distance to two fixed reference structures
 *  basepair distance to two fixed reference structures
 */

#include "data_structures.h"

#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif

/**
 *  \brief Get a structure of type TwoDfold_vars prefilled with current global settings
 * 
 *  This function returns a datastructure of type TwoDfold_vars.
 *  The data fields inside the TwoDfold_vars are prefilled by global settings and all memory
 *  allocations necessary to start a computation are already done for the convenience of the user
 * 
 *  \note Make sure that the reference structures are compatible with the sequence according to Watson-Crick- and Wobble-base pairing
 * 
 *  \see destroy_TwoDfold_variables(), TwoDfold(), TwoDfold_circ
 * 
 *  \param seq          The RNA sequence
 *  \param structure1   The first reference structure in dot-bracket notation
 *  \param structure2   The second reference structure in dot-bracket notation
 *  \param circ         A switch to indicate the assumption to fold a circular instead of linear RNA (0=OFF, 1=ON)
 *  \returns            A datastructure prefilled with folding options and allocated memory
 */
TwoDfold_vars     *get_TwoDfold_variables(const char *seq, const char *structure1, const char *structure2, int circ);

/**
 *  \brief Destroy a TwoDfold_vars datastructure without memory loss
 * 
 *  This function free's all allocated memory that depends on the datastructure given.
 * 
 *  \see get_TwoDfold_variables()
 * 
 *  \param our_variables  A pointer to the datastructure to be destroyed
 */
void              destroy_TwoDfold_variables(TwoDfold_vars *our_variables);

/**
 * 
 */
DEPRECATED(TwoDfold_solution **TwoDfold(TwoDfold_vars *our_variables, int distance1, int distance2));

/**
 * 
 */
TwoDfold_solution *TwoDfoldList(TwoDfold_vars *vars, int distance1, int distance2);

/* function for Pathfinder.c */
/**
 * 
 */
char *TwoDfold_backtrack_f5(unsigned int j, unsigned int k, unsigned int l, TwoDfold_vars *vars);

#endif