RNAlib-2.4.10
LPfold.h
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1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H
2 #define VIENNA_RNA_PACKAGE_LPFOLD_H
3 
4 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
5 
17 #include <ViennaRNA/params/basic.h>
19 
20 #ifdef VRNA_WARN_DEPRECATED
21 # if defined(__clang__)
22 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
23 # elif defined(__GNUC__)
24 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
25 # else
26 # define DEPRECATED(func, msg) func
27 # endif
28 #else
29 # define DEPRECATED(func, msg) func
30 #endif
31 
39 DEPRECATED(void update_pf_paramsLP(int length),
40 "This function is obsolete");
41 
42 
49 DEPRECATED(void update_pf_paramsLP_par(int length,
50  vrna_exp_param_t *parameters),
51 "Use the new API with vrna_folc_compound_t instead");
52 
53 
91 DEPRECATED(vrna_ep_t *pfl_fold(char *sequence,
92  int winSize,
93  int pairSize,
94  float cutoffb,
95  double **pU,
96  vrna_ep_t **dpp2,
97  FILE *pUfp,
98  FILE *spup),
99 "Use vrna_pfl_fold(), vrna_pfl_fold_cb(), vrna_pfl_fold_up(), or vrna_pfl_fold_up_cb() instead");
100 
101 
108 DEPRECATED(vrna_ep_t *pfl_fold_par(char *sequence,
109  int winSize,
110  int pairSize,
111  float cutoffb,
112  double **pU,
113  vrna_ep_t **dpp2,
114  FILE *pUfp,
115  FILE *spup,
116  vrna_exp_param_t *parameters),
117 "Use the new API and vrna_probs_window() instead");
118 
119 
120 DEPRECATED(void putoutpU_prob_par(double **pU,
121  int length,
122  int ulength,
123  FILE *fp,
124  int energies,
125  vrna_exp_param_t *parameters),
126 "");
127 
128 
143 DEPRECATED(void putoutpU_prob(double **pU,
144  int length,
145  int ulength,
146  FILE *fp,
147  int energies),
148 "");
149 
150 
151 DEPRECATED(void putoutpU_prob_bin_par(double **pU,
152  int length,
153  int ulength,
154  FILE *fp,
155  int energies,
156  vrna_exp_param_t *parameters),
157 "");
158 
159 
174 DEPRECATED(void putoutpU_prob_bin(double **pU,
175  int length,
176  int ulength,
177  FILE *fp,
178  int energies),
179 "");
180 
181 
187 DEPRECATED(void init_pf_foldLP(int length),
188 "This function is obsolete");
189 
190 #endif
191 
192 #endif
void update_pf_paramsLP(int length)
vrna_ep_t * pfl_fold(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup)
Compute partition functions for locally stable secondary structures.
Various data structures and pre-processor macros.
void init_pf_foldLP(int length)
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:102
Functions to deal with sets of energy parameters.
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a file.
vrna_ep_t * pfl_fold_par(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup, vrna_exp_param_t *parameters)
Compute partition functions for locally stable secondary structures.
Partition function and equilibrium probability implementation for the sliding window algorithm...
void putoutpU_prob_bin(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a binary file.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:358