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# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h

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    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