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

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

diff --git a/binaries/src/ViennaRNA/H/params.h b/binaries/src/ViennaRNA/H/params.h
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+++ b/binaries/src/ViennaRNA/H/params.h
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+#ifndef __VIENNA_RNA_PACKAGE_PARAMS_H__
+#define __VIENNA_RNA_PACKAGE_PARAMS_H__
+
+#include "energy_const.h"
+#include "data_structures.h"
+
+#ifdef __GNUC__
+#define DEPRECATED(func) func __attribute__ ((deprecated))
+#else
+#define DEPRECATED(func) func
+#endif
+
+/**
+ *  \addtogroup energy_parameters
+ *  \brief All relevant functions to retrieve and copy precalculated energy parameter sets as well as
+ *  reading/writing the energy parameter set from/to file(s).
+ *
+ *  This module covers all relevant functions for precalculation of the energy parameters
+ *  necessary for the folding routines provided by RNAlib. Furthermore, the energy parameter set
+ *  in the RNAlib can be easily exchanged by a user-defined one. It is also possible to write the
+ *  current energy parameter set into a text file.
+ *  @{
+ *
+ *  \file params.h
+ */
+
+/**
+ * \brief Get precomputed energy contributions for all the known loop types
+ *
+ *  \note OpenMP: This function relies on several global model settings variables and thus is
+ *        not to be considered threadsafe. See get_scaled_parameters() for a completely threadsafe
+ *        implementation.
+ *
+ * \return     A set of precomputed energy contributions
+ */
+paramT *scale_parameters(void);
+
+/**
+ * \brief Get precomputed energy contributions for all the known loop types
+ *
+ *  Call this function to retrieve precomputed energy contributions, i.e. scaled
+ *  according to the temperature passed. Furthermore, this function assumes a
+ *  data structure that contains the model details as well, such that subsequent
+ *  folding recursions are able to retrieve the correct model settings
+ *
+ *  \see #model_detailsT, set_model_details()
+ *
+ *  \param temperature  The temperature in degrees Celcius
+ *  \param md           The model details
+ *  \return             precomputed energy contributions and model settings
+ */
+paramT *get_scaled_parameters(double temperature,
+                              model_detailsT md);
+
+paramT *get_parameter_copy(paramT *par);
+
+/**
+ *  get a datastructure of type \ref pf_paramT which contains
+ *  the Boltzmann weights of several energy parameters scaled
+ *  according to the current temperature
+ *  \return The datastructure containing Boltzmann weights for use in partition function calculations
+ */
+pf_paramT *get_scaled_pf_parameters(void);
+
+/**
+ *  \brief Get precomputed Boltzmann factors of the loop type
+ *  dependent energy contributions with independent thermodynamic
+ *  temperature
+ *
+ *  This function returns a data structure that contains
+ *  all necessary precalculated Boltzmann factors for each
+ *  loop type contribution.<br>
+ *  In contrast to get_scaled_pf_parameters(), this function
+ *  enables setting of independent temperatures for both, the
+ *  individual energy contributions as well as the thermodynamic
+ *  temperature used in
+ *  \f$ exp(-\Delta G / kT) \f$
+ *
+ *  \see get_scaled_pf_parameters(), get_boltzmann_factor_copy()
+ *
+ *  \param  temperature   The temperature in degrees Celcius used for (re-)scaling the energy contributions
+ *  \param  betaScale     A scaling value that is used as a multiplication factor for the absolute
+ *                        temperature of the system
+ *  \param  md            The model details to be used
+ *  \param  pf_scale      The scaling factor for the Boltzmann factors
+ *  \return               A set of precomputed Boltzmann factors
+ */
+pf_paramT *get_boltzmann_factors( double temperature,
+                                  double betaScale,
+                                  model_detailsT md,
+                                  double pf_scale);
+
+/**
+ *  \brief Get a copy of already precomputed Boltzmann factors
+ *
+ *  \see get_boltzmann_factors(), get_scaled_pf_parameters()
+ *
+ *  \param  parameters  The input data structure that shall be copied
+ *  \return             A copy of the provided Boltzmann factor dataset
+ */
+pf_paramT *get_boltzmann_factor_copy(pf_paramT *parameters);
+
+/**
+ *  \brief Get precomputed Boltzmann factors of the loop type
+ *  dependent energy contributions (alifold variant)
+ *
+ */
+pf_paramT *get_scaled_alipf_parameters(unsigned int n_seq);
+
+/**
+ *  \brief Get precomputed Boltzmann factors of the loop type
+ *  dependent energy contributions (alifold variant) with
+ *  independent thermodynamic temperature
+ *
+ */
+PUBLIC pf_paramT *get_boltzmann_factors_ali(unsigned int n_seq,
+                                            double temperature,
+                                            double betaScale,
+                                            model_detailsT md,
+                                            double pf_scale);
+
+/**
+ *  @}
+ */
+
+DEPRECATED(paramT     *copy_parameters(void));
+DEPRECATED(paramT     *set_parameters(paramT *dest));
+DEPRECATED(pf_paramT  *scale_pf_parameters(void));
+DEPRECATED(pf_paramT  *copy_pf_param(void));
+DEPRECATED(pf_paramT  *set_pf_param(paramT *dest));
+
+
+
+#endif