RNAlib-2.1.1: /mount/gensoft2/src/ViennaRNA/ViennaRNA-2.1.1/H/alifold.h Source File

00001 #ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__
00002 #define __VIENNA_RNA_PACKAGE_ALIFOLD_H__
00003 
00004 #include "data_structures.h"
00005 
00043 extern  double  cv_fact;
00052 extern  double  nc_fact;
00053 
00054 /*
00055 ##############################################
00056 # MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #
00057 ##############################################
00058 */
00059 
00066 void update_alifold_params(void);
00067 
00068 
00086 float  alifold( const char **strings,
00087                 char *structure);
00088 
00089 
00100 float  circalifold( const char **strings,
00101                     char *structure);
00102 
00109 void    free_alifold_arrays(void);
00110 
00122 int get_mpi(char *Alseq[],
00123             int n_seq,
00124             int length,
00125             int *mini);
00126 
00133 float   **readribosum(char *name);
00134 
00148 float   energy_of_alistruct(const char **sequences,
00149                             const char *structure,
00150                             int n_seq,
00151                             float *energy);
00152 
00153 float   energy_of_ali_gquad_structure(const char **sequences,
00154                                       const char *structure,
00155                                       int n_seq,
00156                                       float *energy);
00157 
00158 /*
00159 #############################################################
00160 # some helper functions that might be useful in the library #
00161 #############################################################
00162 */
00163 
00180 void encode_ali_sequence( const char *sequence,
00181                           short *S,
00182                           short *s5,
00183                           short *s3,
00184                           char *ss,
00185                           unsigned short *as,
00186                           int circ);
00187 
00205 void  alloc_sequence_arrays(const char **sequences,
00206                             short ***S,
00207                             short ***S5,
00208                             short ***S3,
00209                             unsigned short ***a2s,
00210                             char ***Ss,
00211                             int circ);
00212 
00229 void  free_sequence_arrays( unsigned int n_seq,
00230                             short ***S,
00231                             short ***S5,
00232                             short ***S3,
00233                             unsigned short ***a2s,
00234                             char ***Ss);
00235 
00236 /*
00237 #############################################################
00238 # PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #
00239 #############################################################
00240 */
00241 
00242 
00265 float alipf_fold_par( const char **sequences,
00266                       char *structure,
00267                       plist **pl,
00268                       pf_paramT *parameters,
00269                       int calculate_bppm,
00270                       int is_constrained,
00271                       int is_circular);
00272 
00289 float alipf_fold( const char **sequences,
00290                   char *structure,
00291                   plist **pl);
00292 
00303 float alipf_circ_fold(const char **sequences,
00304                       char *structure,
00305                       plist **pl);
00306 
00307 
00319 FLT_OR_DBL *export_ali_bppm(void);
00320 
00327 void  free_alipf_arrays(void);
00328 
00344 char  *alipbacktrack(double *prob);
00345 
00346 
00367 int get_alipf_arrays(short ***S_p,
00368          short ***S5_p,
00369          short ***S3_p,
00370          unsigned short ***a2s_p,
00371          char ***Ss_p,
00372          FLT_OR_DBL **qb_p,
00373          FLT_OR_DBL **qm_p,
00374          FLT_OR_DBL **q1k_p,
00375          FLT_OR_DBL **qln_p,
00376          short **pscore);
00377 
00378 #endif