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alifold.h
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1 #ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__
2 #define __VIENNA_RNA_PACKAGE_ALIFOLD_H__
3
4 #include "data_structures.h"
5
43 extern double cv_fact;
52 extern double nc_fact;
53
54 /*
55 ##############################################
56 # MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #
57 ##############################################
58 */
59
66 void update_alifold_params(void);
67
68
86 float alifold( const char **strings,
87 char *structure);
88
89
100 float circalifold( const char **strings,
101 char *structure);
102
109 void free_alifold_arrays(void);
110
122 int get_mpi(char *Alseq[],
123 int n_seq,
124 int length,
125 int *mini);
126
133 float **readribosum(char *name);
134
148 float energy_of_alistruct(const char **sequences,
149 const char *structure,
150 int n_seq,
151 float *energy);
152
153 float energy_of_ali_gquad_structure(const char **sequences,
154 const char *structure,
155 int n_seq,
156 float *energy);
157
158 /*
159 #############################################################
160 # some helper functions that might be useful in the library #
161 #############################################################
162 */
163
180 void encode_ali_sequence( const char *sequence,
181 short *S,
182 short *s5,
183 short *s3,
184 char *ss,
185 unsigned short *as,
186 int circ);
187
205 void alloc_sequence_arrays(const char **sequences,
206 short ***S,
207 short ***S5,
208 short ***S3,
209 unsigned short ***a2s,
210 char ***Ss,
211 int circ);
212
229 void free_sequence_arrays( unsigned int n_seq,
230 short ***S,
231 short ***S5,
232 short ***S3,
233 unsigned short ***a2s,
234 char ***Ss);
235
236 /*
237 #############################################################
238 # PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #
239 #############################################################
240 */
241
242
265 float alipf_fold_par( const char **sequences,
266 char *structure,
267 plist **pl,
268 pf_paramT *parameters,
269 int calculate_bppm,
270 int is_constrained,
271 int is_circular);
272
289 float alipf_fold( const char **sequences,
290 char *structure,
291 plist **pl);
292
303 float alipf_circ_fold(const char **sequences,
304 char *structure,
305 plist **pl);
306
307
319 FLT_OR_DBL *export_ali_bppm(void);
320
327 void free_alipf_arrays(void);
328
344 char *alipbacktrack(double *prob);
345
346
367 int get_alipf_arrays(short ***S_p,
368 short ***S5_p,
369 short ***S3_p,
370 unsigned short ***a2s_p,
371 char ***Ss_p,
372 FLT_OR_DBL **qb_p,
373 FLT_OR_DBL **qm_p,
374 FLT_OR_DBL **q1k_p,
375 FLT_OR_DBL **qln_p,
376 short **pscore);
377
378 #endif