#ifndef VIENNA_RNA_PACKAGE_MODEL_H
#define VIENNA_RNA_PACKAGE_MODEL_H

/**
 *  @file     model.h
 *  @ingroup  model_details
 *  @brief    The model details data structure and its corresponding modifiers
 */

/**
 *  @addtogroup   model_details
 *  @{
 */

#ifndef NBASES
#define NBASES 8
#endif

/** @brief Typename for the model details data structure #vrna_md_s */
typedef struct vrna_md_s vrna_md_t;

/**
 *  @brief
 *  @htmlonly Default temperature for structure prediction and free energy evaluation in &#176C @endhtmlonly
 *  @latexonly Default temperature for structure prediction and free energy evaluation in $^\circ C$ @endlatexonly
 *
 *  @see  #vrna_md_t.temperature, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_TEMPERATURE    37.0

/**
 *  @brief  Default scaling factor for partition function computations
 *
 *  @see  #vrna_exp_param_t.pf_scale, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_PF_SCALE       -1

/**
 *  @brief  Default scaling factor for absolute thermodynamic temperature in Boltzmann factors
 *
 *  @see    #vrna_exp_param_t.alpha, #vrna_md_t.betaScale, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_BETA_SCALE     1.

/**
 *  @brief  Default dangling end model
 *
 *  @see  #vrna_md_t.dangles, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_DANGLES        2

/**
 *  @brief  Default model behavior for lookup of special tri-, tetra-, and hexa-loops
 *
 *  @see    #vrna_md_t.special_hp, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_SPECIAL_HP     1

/**
 *  @brief  Default model behavior for so-called 'lonely pairs'
 *
 *  @see    #vrna_md_t.noLP, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_NO_LP          0

/**
 *  @brief  Default model behavior for G-U base pairs
 *
 *  @see    #vrna_md_t.noGU, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_NO_GU          0

/**
 *  @brief  Default model behavior for G-U base pairs closing a loop
 *
 *  @see    #vrna_md_t.noGUclosure, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE  0

/**
 *  @brief  Default model behavior to treat a molecule as a circular RNA (DNA)
 *  @see    #vrna_md_t.circ, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_CIRC           0

/**
 *  @brief  Default model behavior regarding the treatment of G-Quadruplexes
 *
 *  @see    #vrna_md_t.gquad, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_GQUAD          0

/**
 *  @brief  Default behavior of the model regarding unique multi-branch loop decomposition
 *
 *  @see    #vrna_md_t.uniq_ML, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_UNIQ_ML        0

/**
 *  @brief  Default model behavior on which energy set to use
 *
 *  @see    #vrna_md_t.energy_set, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_ENERGY_SET     0

/**
 *  @brief  Default model behavior with regards to backtracking of structures
 *  @see    #vrna_md_t.backtrack, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_BACKTRACK      1

/**
 *  @brief  Default model behavior on what type of backtracking to perform
 *
 *  @see    #vrna_md_t.backtrack_type, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'

/**
 *  @brief  Default model behavior with regards to computing base pair probabilities
 *
 *  @see    #vrna_md_t.compute_bpp, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_COMPUTE_BPP    1

/**
 *  @brief  Default model behavior for the allowed maximum base pair span
 *
 *  @see    #vrna_md_t.max_bp_span, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_MAX_BP_SPAN    -1

/**
 *  @brief  Default model behavior for the sliding window approach
 *
 *  @see    #vrna_md_t.window_size, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_WINDOW_SIZE    -1

/**
 *  @brief  Default model behavior on how to evaluate the energy contribution of multi-branch loops
 *
 *  @see    #vrna_md_t.logML, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_LOG_ML         0

/**
 *  @brief  Default model behavior for consensus structure energy evaluation
 *  @see    #vrna_md_t.oldAliEn, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_ALI_OLD_EN     0

/**
 *  @brief  Default model behavior for consensus structure co-variance contribution assessment
 *
 *  @see    #vrna_md_t.ribo, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_ALI_RIBO       0

/**
 *  @brief  Default model behavior for weighting the co-variance score in consensus structure prediction
 *
 *  @see    #vrna_md_t.cv_fact, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_ALI_CV_FACT    1.

/** @brief  Default model behavior for weighting the nucleotide conservation? in consensus structure prediction
 *
 *  @see    #vrna_md_t.nc_fact, vrna_md_defaults_reset(), vrna_md_set_default()
 */
#define VRNA_MODEL_DEFAULT_ALI_NC_FACT    1.


#define VRNA_MODEL_DEFAULT_PF_SMOOTH      1

/**
 *  @brief  Default model salt concentration (M)
 */
#define VRNA_MODEL_DEFAULT_SALT           1.021


/**
 *  @brief  Default model lower bound of multiloop size for salt correction fiting
 */
#define VRNA_MODEL_DEFAULT_SALT_MLLOWER    6


/**
 *  @brief  Default model upper bound of multiloop size for salt correction fiting
 */
#define VRNA_MODEL_DEFAULT_SALT_MLUPPER    24


/**
 *  @brief  Default model value to turn off user-provided salt correction for duplex initializtion
 */
#define VRNA_MODEL_DEFAULT_SALT_DPXINIT       99999

#define VRNA_MODEL_SALT_DPXINIT_FACT_RNA      -45.324
#define VRNA_MODEL_SALT_DPXINIT_FACT_DNA      -58.389


#define VRNA_MODEL_DEFAULT_SALT_DPXINIT_FACT  VRNA_MODEL_SALT_DPXINIT_FACT_RNA

/* Geometric parameters for RNA and DNA */

#define VRNA_MODEL_HELICAL_RISE_RNA   2.8
#define VRNA_MODEL_HELICAL_RISE_DNA   3.4
/**
 *  @brief  Default helical rise
 */
#define VRNA_MODEL_DEFAULT_HELICAL_RISE   VRNA_MODEL_HELICAL_RISE_RNA

#define VRNA_MODEL_BACKBONE_LENGTH_RNA   6.0
#define VRNA_MODEL_BACKBONE_LENGTH_DNA   6.76
/**
 *  @brief  Default backbone length
 */
#define VRNA_MODEL_DEFAULT_BACKBONE_LENGTH   VRNA_MODEL_BACKBONE_LENGTH_RNA


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

#ifndef MAXALPHA
/**
 *  @brief Maximal length of alphabet
 */
#define MAXALPHA              20
#endif

#endif

/**
 *  @brief The data structure that contains the complete model details used throughout the calculations
 *
 *  For convenience reasons, we provide the type name #vrna_md_t to address this data structure
 *  without the use of the struct keyword
 *
 *  @see  vrna_md_set_default(), set_model_details(), vrna_md_update(), #vrna_md_t
 *
 */
struct vrna_md_s {
  double  temperature;                      /**<  @brief  The temperature used to scale the thermodynamic parameters */
  double  betaScale;                        /**<  @brief  A scaling factor for the thermodynamic temperature of the Boltzmann factors */
  int     pf_smooth;                        /**<  @brief  A flat specifying whether energies in Boltzmann factors need to be smoothed */
  int     dangles;                          /**<  @brief  Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
                                             *
                                             *    If set to 0 no stabilizing energies are assigned to bases adjacent to
                                             *    helices in free ends and multiloops (so called dangling ends). Normally
                                             *    (dangles = 1) dangling end energies are assigned only to unpaired
                                             *    bases and a base cannot participate simultaneously in two dangling ends. In
                                             *    the partition function algorithm vrna_pf() these checks are neglected.
                                             *    To provide comparability between free energy minimization and partition function
                                             *    algorithms, the default setting is 2.
                                             *    This treatment of dangling ends gives more favorable energies to helices
                                             *    directly adjacent to one another, which can be beneficial since such
                                             *    helices often do engage in stabilizing interactions through co-axial
                                             *    stacking.\n
                                             *    If set to 3 co-axial stacking is explicitly included for
                                             *    adjacent helices in multiloops. The option affects only mfe folding
                                             *    and energy evaluation (vrna_mfe() and vrna_eval_structure()), as
                                             *    well as suboptimal folding (vrna_subopt()) via re-evaluation of energies.
                                             *    Co-axial stacking with one intervening mismatch is not considered so far.
                                             *    Note, that some function do not implement all dangle model but only a subset of
                                             *    (0,1,2,3). In particular, partition function algorithms can only handle
                                             *    0 and 2. Read the documentation of the particular recurrences or
                                             *    energy evaluation function for information about the provided dangle
                                             *    model.
                                             */
  int     special_hp;                       /**<  @brief  Include special hairpin contributions for tri, tetra and hexaloops */
  int     noLP;                             /**<  @brief  Only consider canonical structures, i.e. no 'lonely' base pairs */
  int     noGU;                             /**<  @brief  Do not allow GU pairs */
  int     noGUclosure;                      /**<  @brief  Do not allow loops to be closed by GU pair */
  int     logML;                            /**<  @brief  Use logarithmic scaling for multiloops */
  int     circ;                             /**<  @brief  Assume RNA to be circular instead of linear */
  int     gquad;                            /**<  @brief  Include G-quadruplexes in structure prediction */
  int     uniq_ML;                          /**<  @brief  Flag to ensure unique multi-branch loop decomposition during folding */
  int     energy_set;                       /**<  @brief  Specifies the energy set that defines set of compatible base pairs */
  int     backtrack;                        /**<  @brief  Specifies whether or not secondary structures should be backtraced */
  char    backtrack_type;                   /**<  @brief  Specifies in which matrix to backtrack */
  int     compute_bpp;                      /**<  @brief  Specifies whether or not backward recursions for base pair probability (bpp) computation will be performed */
  char    nonstandards[64];                 /**<  @brief  contains allowed non standard bases */
  int     max_bp_span;                      /**<  @brief  maximum allowed base pair span */

  int     min_loop_size;                    /**<  @brief  Minimum size of hairpin loops
                                             *
                                             *    The default value for this field is #TURN, however, it may
                                             *    be 0 in cofolding context.
                                             */
  int     window_size;                      /**<  @brief  Size of the sliding window for locally optimal structure prediction */
  int     oldAliEn;                         /**<  @brief  Use old alifold energy model */
  int     ribo;                             /**<  @brief  Use ribosum scoring table in alifold energy model */
  double  cv_fact;                          /**<  @brief  Co-variance scaling factor for consensus structure prediction */
  double  nc_fact;                          /**<  @brief  Scaling factor to weight co-variance contributions of non-canonical pairs */
  double  sfact;                            /**<  @brief  Scaling factor for partition function scaling */
  int     rtype[8];                         /**<  @brief  Reverse base pair type array */
  short   alias[MAXALPHA + 1];              /**<  @brief  alias of an integer nucleotide representation */
  int     pair[MAXALPHA + 1][MAXALPHA + 1]; /**<  @brief  Integer representation of a base pair */
  float   pair_dist[7][7];                  /**<  @brief  Base pair dissimilarity, a.k.a. distance matrix */
  double  salt;                             /**<  @brief  Salt (monovalent) concentration (M) in buffer */
  int     saltMLLower;                      /**<  @brief  Lower bound of multiloop size to use in loop salt correction linear fitting */
  int     saltMLUpper;                      /**<  @brief  Upper bound of multiloop size to use in loop salt correction linear fitting */
  int     saltDPXInit;                      /**<  @brief  User-provided salt correction for duplex initialization (in dcal/mol).
                                             *    If set to 99999 the default salt correction is used.
                                             *    If set to 0 there is no salt correction for duplex initialization.
                                             */
  float   saltDPXInitFact;                  /**<  @brief  */
  float   helical_rise;                     /**<  @brief  */
  float   backbone_length;                  /**<  @brief  */
};


/**
 * @brief Apply default model details to a provided #vrna_md_t data structure
 *
 *  Use this function to initialize a #vrna_md_t data structure with
 *  its default values
 *
 *  @param md A pointer to the data structure that is about to be initialized
 */
void
vrna_md_set_default(vrna_md_t *md);


/**
 *  @brief Update the model details data structure
 *
 *  This function should be called after changing the vrna_md_t.energy_set attribute
 *  since it re-initializes base pairing related arrays within the #vrna_md_t data
 *  structure. In particular, #vrna_md_t.pair, #vrna_md_t.alias, and #vrna_md_t.rtype
 *  are set to the values that correspond to the specified #vrna_md_t.energy_set
 *  option
 *
 *  @see  #vrna_md_t, #vrna_md_t.energy_set, #vrna_md_t.pair, #vrna_md_t.rtype,
 *        #vrna_md_t.alias, vrna_md_set_default()
 */
void
vrna_md_update(vrna_md_t *md);


/**
 *  @brief Copy/Clone a #vrna_md_t model
 *
 *  Use this function to clone a given model either inplace (target container @p md_to
 *  given) or create a copy by cloning the source model and returning it (@p md_to == NULL).
 *
 *  @param md_to    The model to be overwritten (if non-NULL and @p md_to != @p md_from)
 *  @param md_from  The model to copy (if non-NULL)
 *  @return         A pointer to the copy model (or NULL if @p md_from == NULL)
 */
vrna_md_t *
vrna_md_copy(vrna_md_t        *md_to,
             const vrna_md_t  *md_from);


/**
 *  @brief  Get a corresponding commandline parameter string of the options in a #vrna_md_t
 *
 *  @note This function is not threadsafe!
 */
char *
vrna_md_option_string(vrna_md_t *md);


void
vrna_md_set_nonstandards(vrna_md_t  *md,
                         const char *ns_bases);


/**
 *  @brief  Reset the global default model details to a specific set of parameters, or their initial values
 *
 *  This function resets the global default model details to their initial values,
 *  i.e. as specified by the ViennaRNA Package release, upon passing NULL as argument.
 *  Alternatively it resets them according to a set of provided parameters.
 *
 *  @note The global default parameters affect all function calls of RNAlib where
 *        model details are not explicitly provided. Hence, any change of them
 *        is not considered threadsafe
 *
 *  @warning  This function first resets the global default settings to factory
 *            defaults, and only then applies user provided settings (if any).
 *            User settings that do not meet specifications are skipped.
 *
 *  @see  vrna_md_set_default(), #vrna_md_t
 *
 *  @param md_p A set of model details to use as global default (if NULL is passed, factory defaults are restored)
 */
void
vrna_md_defaults_reset(vrna_md_t *md_p);


/**
 *  @brief  Set default temperature for energy evaluation of loops
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_TEMPERATURE
 *
 *  @param T  Temperature in centigrade
 */
void
vrna_md_defaults_temperature(double T);


/**
 *  @brief  Get default temperature for energy evaluation of loops
 *
 *  @see vrna_md_defaults_temperature(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_TEMPERATURE
 *
 *  @return  The global default settings for temperature in centigrade
 */
double
vrna_md_defaults_temperature_get(void);


/**
 *  @brief  Set default scaling factor of thermodynamic temperature in Boltzmann factors
 *
 *  Bolzmann factors are then computed as @f$ exp(-E / (b \cdot kT))@f$.
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BETA_SCALE
 *
 *  @param b  The scaling factor, default is 1.0
 */
void
vrna_md_defaults_betaScale(double b);


/**
 *  @brief  Get default scaling factor of thermodynamic temperature in Boltzmann factors
 *
 *  @see vrna_md_defaults_betaScale(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BETA_SCALE
 *
 *  @return  The global default thermodynamic temperature scaling factor
 */
double
vrna_md_defaults_betaScale_get(void);


void
vrna_md_defaults_pf_smooth(int s);


int
vrna_md_defaults_pf_smooth_get(void);


/**
 *  @brief  Set default dangle model for structure prediction
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_DANGLES
 *
 *  @param d  The dangle model
 */
void
vrna_md_defaults_dangles(int d);


/**
 *  @brief  Get default dangle model for structure prediction
 *
 *  @see vrna_md_defaults_dangles(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_DANGLES
 *
 *  @return The global default settings for the dangle model
 */
int
vrna_md_defaults_dangles_get(void);


/**
 *  @brief  Set default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_SPECIAL_HP
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_special_hp(int flag);


/**
 *  @brief  Get default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.
 *
 *  @see vrna_md_defaults_special_hp(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_SPECIAL_HP
 *
 *  @return  The global default settings for the treatment of special hairpin loops
 */
int
vrna_md_defaults_special_hp_get(void);


/**
 *  @brief  Set default behavior for prediction of canonical secondary structures
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_LP
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_noLP(int flag);


/**
 *  @brief  Get default behavior for prediction of canonical secondary structures
 *
 *  @see vrna_md_defaults_noLP(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_LP
 *
 *  @return  The global default settings for predicting canonical secondary structures
 */
int
vrna_md_defaults_noLP_get(void);


/**
 *  @brief  Set default behavior for treatment of G-U wobble pairs
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_GU
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_noGU(int flag);


/**
 *  @brief  Get default behavior for treatment of G-U wobble pairs
 *
 *  @see vrna_md_defaults_noGU(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_GU
 *
 *  @return The global default settings for treatment of G-U wobble pairs
 */
int
vrna_md_defaults_noGU_get(void);


/**
 *  @brief  Set default behavior for G-U pairs as closing pair for loops
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_GU_CLOSURE
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_noGUclosure(int flag);


/**
 *  @brief  Get default behavior for G-U pairs as closing pair for loops
 *
 *  @see vrna_md_defaults_noGUclosure(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_GU_CLOSURE
 *
 *  @return The global default settings for treatment of G-U pairs closing a loop
 */
int
vrna_md_defaults_noGUclosure_get(void);


/**
 *  @brief  Set default behavior recomputing free energies of multi-branch loops using a logarithmic model
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_LOG_ML
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_logML(int flag);


/**
 *  @brief  Get default behavior recomputing free energies of multi-branch loops using a logarithmic model
 *
 *  @see vrna_md_defaults_logML(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_LOG_ML
 *
 *  @return The global default settings for logarithmic model in multi-branch loop free energy evaluation
 */
int
vrna_md_defaults_logML_get(void);


/**
 *  @brief  Set default behavior whether input sequences are circularized
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_CIRC
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_circ(int flag);


/**
 *  @brief  Get default behavior whether input sequences are circularized
 *
 *  @see vrna_md_defaults_circ(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_CIRC
 *
 *  @return The global default settings for treating input sequences as circular
 */
int
vrna_md_defaults_circ_get(void);


/**
 *  @brief  Set default behavior for treatment of G-Quadruplexes
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_GQUAD
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_gquad(int flag);


/**
 *  @brief  Get default behavior for treatment of G-Quadruplexes
 *
 *  @see vrna_md_defaults_gquad(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_GQUAD
 *
 *  @return The global default settings for treatment of G-Quadruplexes
 */
int
vrna_md_defaults_gquad_get(void);


/**
 *  @brief  Set default behavior for creating additional matrix for unique multi-branch loop prediction
 *
 *  @note   Activating this option usually results in higher memory consumption!
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_UNIQ_ML
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_uniq_ML(int flag);


/**
 *  @brief  Get default behavior for creating additional matrix for unique multi-branch loop prediction
 *
 *  @see vrna_md_defaults_uniq_ML(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_UNIQ_ML
 *
 *  @return The global default settings for creating additional matrices for unique multi-branch loop prediction
 */
int
vrna_md_defaults_uniq_ML_get(void);


/**
 *  @brief  Set default energy set
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ENERGY_SET
 *
 *  @param  e   Energy set (0, 1, 2, 3)
 */
void
vrna_md_defaults_energy_set(int e);


/**
 *  @brief  Get default energy set
 *
 *  @see vrna_md_defaults_energy_set(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ENERGY_SET
 *
 *  @return The global default settings for the energy set
 */
int
vrna_md_defaults_energy_set_get(void);


/**
 *  @brief  Set default behavior for whether to backtrack secondary structures
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BACKTRACK
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_backtrack(int flag);


/**
 *  @brief  Get default behavior for whether to backtrack secondary structures
 *
 *  @see vrna_md_defaults_backtrack(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BACKTRACK
 *
 *  @return The global default settings for backtracking structures
 */
int
vrna_md_defaults_backtrack_get(void);


/**
 *  @brief  Set default backtrack type, i.e. which DP matrix is used
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BACKTRACK_TYPE
 *
 *  @param  t   The type ('F', 'C', or 'M')
 */
void
vrna_md_defaults_backtrack_type(char t);


/**
 *  @brief  Get default backtrack type, i.e. which DP matrix is used
 *
 *  @see vrna_md_defaults_backtrack_type(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BACKTRACK_TYPE
 *
 *  @return The global default settings that specify which DP matrix is used for backtracking
 */
char
vrna_md_defaults_backtrack_type_get(void);


/**
 *  @brief  Set the default behavior for whether to compute base pair probabilities after partition function computation
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_COMPUTE_BPP
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_compute_bpp(int flag);


/**
 *  @brief  Get the default behavior for whether to compute base pair probabilities after partition function computation
 *
 *  @see vrna_md_defaults_compute_bpp(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_COMPUTE_BPP
 *
 *  @return The global default settings that specify whether base pair probabilities are computed together with partition function
 */
int
vrna_md_defaults_compute_bpp_get(void);


/**
 *  @brief  Set default maximal base pair span
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_MAX_BP_SPAN
 *
 *  @param  span  Maximal base pair span
 */
void
vrna_md_defaults_max_bp_span(int span);


/**
 *  @brief  Get default maximal base pair span
 *
 *  @see vrna_md_defaults_max_bp_span(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_MAX_BP_SPAN
 *
 *  @return The global default settings for maximum base pair span
 */
int
vrna_md_defaults_max_bp_span_get(void);


/**
 *  @brief  Set default minimal loop size
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #TURN
 *
 *  @param  size  Minimal size, i.e. number of unpaired nucleotides for a hairpin loop
 */
void
vrna_md_defaults_min_loop_size(int size);


/**
 *  @brief  Get default minimal loop size
 *
 *  @see vrna_md_defaults_min_loop_size(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #TURN
 *
 *  @return The global default settings for minimal size of hairpin loops
 */
int
vrna_md_defaults_min_loop_size_get(void);


/**
 *  @brief  Set default window size for sliding window structure prediction approaches
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_WINDOW_SIZE
 *
 *  @param  size  The size of the sliding window
 */
void
vrna_md_defaults_window_size(int size);


/**
 *  @brief  Get default window size for sliding window structure prediction approaches
 *
 *  @see vrna_md_defaults_window_size(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_WINDOW_SIZE
 *
 *  @return The global default settings for the size of the sliding window
 */
int
vrna_md_defaults_window_size_get(void);


/**
 *  @brief  Set default behavior for whether to use old energy model for comparative structure prediction
 *
 *  @note   This option is outdated. Activating the old energy model usually results in worse consensus
 *          structure predictions.
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_OLD_EN
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_oldAliEn(int flag);


/**
 *  @brief  Get default behavior for whether to use old energy model for comparative structure prediction
 *
 *  @see vrna_md_defaults_oldAliEn(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_OLD_EN
 *
 *  @return The global default settings for using old energy model for comparative structure prediction
 */
int
vrna_md_defaults_oldAliEn_get(void);


/**
 *  @brief  Set default behavior for whether to use Ribosum Scoring in comparative structure prediction
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_RIBO
 *
 *  @param  flag  On/Off switch (0 = OFF, else = ON)
 */
void
vrna_md_defaults_ribo(int flag);


/**
 *  @brief  Get default behavior for whether to use Ribosum Scoring in comparative structure prediction
 *
 *  @see vrna_md_defaults_ribo(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_RIBO
 *
 *  @return The global default settings for using Ribosum scoring in comparative structure prediction
 */
int
vrna_md_defaults_ribo_get(void);


/**
 *  @brief  Set the default co-variance scaling factor used in comparative structure prediction
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_CV_FACT
 *
 *  @param  factor  The co-variance factor
 */
void
vrna_md_defaults_cv_fact(double factor);


/**
 *  @brief  Get the default co-variance scaling factor used in comparative structure prediction
 *
 *  @see vrna_md_defaults_cv_fact(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_CV_FACT
 *
 *  @return The global default settings for the co-variance factor
 */
double
vrna_md_defaults_cv_fact_get(void);


/**
 *  @brief
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_NC_FACT
 *
 *  @param factor
 */
void
vrna_md_defaults_nc_fact(double factor);


/**
 *  @brief
 *
 *  @see vrna_md_defaults_nc_fact(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_NC_FACT
 *
 *  @return
 */
double
vrna_md_defaults_nc_fact_get(void);


/**
 *  @brief  Set the default scaling factor used to avoid under-/overflows in partition function computation
 *
 *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t
 *
 *  @param  factor  The scaling factor  (default: 1.07)
 */
void
vrna_md_defaults_sfact(double factor);


/**
 *  @brief  Get the default scaling factor used to avoid under-/overflows in partition function computation
 *
 *  @see vrna_md_defaults_sfact(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t
 *
 *  @return The global default settings of the scaling factor
 */
double
vrna_md_defaults_sfact_get(void);


/**
 *  @brief Set the default salt concentration
 *
 *  @param salt The sodium concentration in M (default: 1.021)
 */
void
vrna_md_defaults_salt(double salt);


/**
 *  @brief Get the default salt concentration
 *  @return The default salt concentration
 */
double
vrna_md_defaults_salt_get(void);


/**
 *  @brief Set the default multiloop size lower bound for loop salt correciton linear fitting
 *
 *  @param lower Size lower bound (number of backbone in loop)
 */
void
vrna_md_defaults_saltMLLower(int lower);


/**
 *  @brief Get the default multiloop size lower bound for loop salt correciton linear fitting
 *  @return The default lower bound
 */
int
vrna_md_defaults_saltMLLower_get(void);


/**
 *  @brief Set the default multiloop size upper bound for loop salt correciton linear fitting
 *
 *  @param upper Size Upper bound (number of backbone in loop)
 */
void
vrna_md_defaults_saltMLUpper(int upper);


/**
 *  @brief Get the default multiloop size upper bound for loop salt correciton linear fitting
 *  @return The default upper bound
 */
int
vrna_md_defaults_saltMLUpper_get(void);


/**
 *  @brief Set user-provided salt correciton for duplex initialization
 *  If value is 99999 the default value from fitting is used
 *
 *  @param value The value of salt correction for duplex initialization (in dcal/mol)
 */
void
vrna_md_defaults_saltDPXInit(int value);


/**
 *  @brief Get user-provided salt correciton for duplex initialization
 *  If value is 99999 the default value from fitting is used
 *
 *  @return The user-provided salt correction for duplex initialization
 */
int
vrna_md_defaults_saltDPXInit_get(void);


void
vrna_md_defaults_saltDPXInitFact(float value);


float
vrna_md_defaults_saltDPXInitFact_get(void);


void
vrna_md_defaults_helical_rise(float value);


float
vrna_md_defaults_helical_rise_get(void);


void
vrna_md_defaults_backbone_length(float value);


float
vrna_md_defaults_backbone_length_get(void);


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

#define model_detailsT        vrna_md_t               /* restore compatibility of struct rename */

/* BEGIN deprecated global variables: */

/**
 *  @brief Rescale energy parameters to a temperature in degC.
 *
 *  Default is 37C. You have to call the update_..._params() functions after
 *  changing this parameter.
 *
 *  @deprecated   Use vrna_md_defaults_temperature(), and vrna_md_defaults_temperature_get()
 *                to change, and read the global default temperature settings
 *
 *  @see vrna_md_defaults_temperature(), vrna_md_defaults_temperature_get(), vrna_md_defaults_reset()
 */
extern double temperature;

/**
 *  @brief A scaling factor used by pf_fold() to avoid overflows.
 *
 *  Should be set to approximately @f$exp{((-F/kT)/length)}@f$, where @f$F@f$ is an estimate
 *  for the ensemble free energy, for example the minimum free energy. You must
 *  call update_pf_params() after changing this parameter.\n
 *  If pf_scale is -1 (the default) , an estimate will be provided
 *  automatically when computing partition functions, e.g. pf_fold()
 *  The automatic estimate is usually insufficient for sequences more
 *  than a few hundred bases long.
 */
extern double pf_scale;

/**
 *  @brief Switch the energy model for dangling end contributions (0, 1, 2, 3)
 *
 *  If set to 0 no stabilizing energies are assigned to bases adjacent to
 *  helices in free ends and multiloops (so called dangling ends). Normally
 *  (dangles = 1) dangling end energies are assigned only to unpaired
 *  bases and a base cannot participate simultaneously in two dangling ends. In
 *  the partition function algorithm pf_fold() these checks are neglected.
 *  If #dangles is set to 2, all folding routines will follow this convention.
 *  This treatment of dangling ends gives more favorable energies to helices
 *  directly adjacent to one another, which can be beneficial since such
 *  helices often do engage in stabilizing interactions through co-axial
 *  stacking.\n
 *  If dangles = 3 co-axial stacking is explicitly included for
 *  adjacent helices in multiloops. The option affects only mfe folding
 *  and energy evaluation (fold() and energy_of_structure()), as
 *  well as suboptimal folding (subopt()) via re-evaluation of energies.
 *  Co-axial stacking with one intervening mismatch is not considered so far.
 *
 *  Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2
 */
extern int dangles;

/**
 *  @brief Include special stabilizing energies for some tri-, tetra- and hexa-loops;
 *
 *  default is 1.
 */
extern int tetra_loop;

/**
 *  @brief Global switch to avoid/allow helices of length 1
 *
 *  Disallow all pairs which can only occur as lonely pairs (i.e. as helix
 *  of length 1). This avoids lonely base pairs in the predicted structures in
 *  most cases.
 */
extern int  noLonelyPairs;

/**
 *  @brief Global switch to forbid/allow GU base pairs at all
 */
extern int  noGU;

/**
 *  @brief GU allowed only inside stacks if set to 1
 */
extern int  no_closingGU;

/**
 *  @brief backward compatibility variable.. this does not effect anything
 */
extern int  circ;

/**
 *  @brief Allow G-quadruplex formation
 */
extern int  gquad;

/**
 *  @brief do ML decomposition uniquely (for subopt)
 */
extern int  uniq_ML;

/**
 *  @brief 0 = BP; 1=any with GC; 2=any with AU-parameter
 *
 *  If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A
 *  pairs B, C pairs D, etc. using either GC (1) or AU parameters (2);
 *  default is 0, you probably don't want to change it.
 */
extern int energy_set;

/**
 *  @brief do backtracking, i.e. compute secondary structures or base pair probabilities
 *
 *  If 0, do not calculate pair probabilities in pf_fold(); this is about
 *  twice as fast. Default is 1.
 */
extern int do_backtrack;

/**
 *  @brief A backtrack array marker for inverse_fold()
 *
 *  If set to 'C': force (1,N) to be paired,
 *  'M' fold as if the sequence were inside a multiloop. Otherwise ('F') the
 *  usual mfe structure is computed.
 */
extern char backtrack_type;

/**
 *  @brief contains allowed non standard base pairs
 *
 *  Lists additional base pairs that will be allowed to form in addition to
 *  GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking
 *  energy of 0.
 */
extern char *nonstandards;

/**
 *  @brief Maximum allowed base pair span
 *
 *  A value of -1 indicates no restriction for distant base pairs.
 */
extern int    max_bp_span;

/**
 *  @brief use old alifold energies (with gaps)
 */
extern int    oldAliEn;

/**
 *  @brief use ribosum matrices
 */
extern int    ribo;

extern double cv_fact;

extern double nc_fact;

/** @brief if nonzero use logarithmic ML energy in energy_of_struct  */
extern int    logML;

/** @brief salt concentration */
extern double salt;

/** @brief Salt correction for duplex initialization */
extern int saltDPXInit;

extern float  helical_rise;
extern float  backbone_length;

/* END deprecated global variables: */

/**
 * @brief Set default model details
 *
 *  Use this function if you wish to initialize a #vrna_md_t data structure with
 *  its default values, i.e. the global model settings as provided by the deprecated
 *  global variables.
 *
 *  @deprecated This function will vanish as soon as backward compatibility of
 *              RNAlib is dropped (expected in version 3).
 *              Use vrna_md_set_default() instead!
 *
 *  @param md A pointer to the data structure that is about to be initialized
 */
void
set_model_details(vrna_md_t *md);


char *
option_string(void);


#endif
/**
 * @}
 */

#endif
