#ifndef __VIENNA_RNA_PACKAGE_LPFOLD_H__
#define __VIENNA_RNA_PACKAGE_LPFOLD_H__

#include "data_structures.h"

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

/**
 *  \file LPfold.h
 *  \brief Function declarations of partition function variants of the Lfold algorithm
 * 
 */

/**
 *  \brief
 * 
 *  \param  length
 */
void update_pf_paramsLP(int length);

void update_pf_paramsLP_par(int length, pf_paramT *parameters);

/**
 *  \brief Compute partition functions for locally stable secondary structures <b>(berni! update me)</b>
 * 
 *  pfl_fold computes partition functions for every window of size
 *  'winSize' possible in a RNA molecule, allowing only pairs with a span
 *  smaller than 'pairSize'. It returns the mean pair probabilities averaged
 *  over all windows containing the pair in 'pl'. 'winSize' should
 *  always be >= 'pairSize'. Note that in contrast to Lfold(),
 *  bases outside of the window do not influence the structure at all. Only
 *  probabilities higher than 'cutoffb' are kept.
 * 
 *  If 'pU' is supplied (i.e is not the NULL pointer), pfl_fold()
 *  will also compute the mean probability that regions of length 'u' and smaller are 
 *  unpaired. The parameter 'u' is supplied in 'pup[0][0]'. On return
 *  the 'pup' array will contain these probabilities, with the entry on
 *  'pup[x][y]' containing the mean probability that x and the y-1
 *  preceding bases are unpaired. The 'pU' array needs to be large
 *  enough to hold n+1 float* entries, where n is the sequence length.
 * 
 *  If an array dpp2 is supplied, the probability of base pair (i,j)
 *  given that there already exists a base pair (i+1,j-1) is also
 *  computed and saved in this array. If pUfp is given (i.e. not NULL), pU
 *  is not saved but put out imediately. If spup is given (i.e. is not NULL),
 *  the pair probabilities in pl are not saved but put out imediately.
 *  \param  sequence  RNA sequence
 *  \param  winSize   size of the window
 *  \param  pairSize  maximum size of base pair
 *  \param  cutoffb   cutoffb for base pairs
 *  \param  pU        array holding all unpaired probabilities   
 *  \param  dpp2  array of dependent pair probabilities    
 *  \param  pUfp     file pointer for pU 
 *  \param  spup     file pointer for pair probabilities   
 *  \return list of pair probabilities       
 */
plist *pfl_fold(char *sequence,
                int winSize,
                int pairSize,
                float cutoffb,
                double **pU,
                struct plist **dpp2,
                FILE *pUfp,
                FILE *spup);


plist *pfl_fold_par(char *sequence,
                    int winSize,
                    int pairSize,
                    float cutoffb,
                    double **pU,
                    struct plist **dpp2,
                    FILE *pUfp,
                    FILE *spup,
                    pf_paramT *parameters);


/**
 *  \brief Writes the unpaired probabilities (pU) or opening energies into a file
 * 
 *  Can write either the unpaired probabilities (accessibilities) pU or
 *  the opening energies -log(pU)kT into a file
 *  \param  pU       pair probabilities
 *  \param  length   length of RNA sequence 
 *  \param  ulength  maximum length of unpaired stretch 
 *  \param  fp file pointer of destination file       
 *  \param  energies  switch to put out as  opening energies 
 */
void    putoutpU_prob(double **pU,
                      int length,
                      int ulength,
                      FILE *fp,
                      int energies);

/**
 *  \brief Writes the unpaired probabilities (pU) or opening energies into a binary file 
 * 
 *  Can write either the unpaired probabilities (accessibilities) pU or
 *  the opening energies -log(pU)kT into a file
 *  \param  pU       pair probabilities
 *  \param  length   length of RNA sequence 
 *  \param  ulength  maximum length of unpaired stretch 
 *  \param  fp file pointer of destination file       
 *  \param  energies  switch to put out as  opening energies 
 */
void    putoutpU_prob_bin(double **pU,
                          int length,
                          int ulength,
                          FILE *fp,
                          int energies);

/**
 *  Dunno if this function was ever used by external programs linking to RNAlib, but it
 *  was declared PUBLIC before.
 *  Anyway, never use this function as it will be removed soon and does nothing at all
 */
DEPRECATED(void init_pf_foldLP(int length));

#endif