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# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h

Go to the documentation of this file.

    00001 /*
    00002       minimum free energy
    00003       RNA secondary structure with
    00004       basepair distance d to reference structure prediction
    00005
    00006 */
    00007 #ifndef __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
    00008 #define __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
    00009
    00010 #include "data_structures.h"
    00011
    00012 #ifdef __GNUC__
    00013 #define DEPRECATED(func) func __attribute__ ((deprecated))
    00014 #else
    00015 #define DEPRECATED(func) func
    00016 #endif
    00017
    00042 TwoDpfold_vars  *get_TwoDpfold_variables( const char *seq,
    00043                                           const char *structure1,
    00044                                           char *structure2,
    00045                                           int circ);
    00046
    00059 TwoDpfold_vars  *get_TwoDpfold_variables_from_MFE(TwoDfold_vars *mfe_vars);
    00060
    00071 void            destroy_TwoDpfold_variables(TwoDpfold_vars *vars);
    00072
    00094 TwoDpfold_solution  *TwoDpfoldList( TwoDpfold_vars *vars,
    00095                                     int maxDistance1,
    00096                                     int maxDistance2);
    00097  /* End of group kl_neighborhood_pf */
    00099
    00123 char            *TwoDpfold_pbacktrack(TwoDpfold_vars *vars,
    00124                                       int d1,
    00125                                       int d2);
    00126
    00146 char            *TwoDpfold_pbacktrack5( TwoDpfold_vars *vars,
    00147                                           int d1,
    00148                                           int d2,
    00149                                           unsigned int length);
    00150  /* End of group kl_neighborhood_stochbt */
    00152
    00158 DEPRECATED(FLT_OR_DBL          **TwoDpfold(TwoDpfold_vars *our_variables,
    00159                                 int maxDistance1,
    00160                                 int maxDistance2));
    00161
    00167 DEPRECATED(FLT_OR_DBL          **TwoDpfold_circ(
    00168                                 TwoDpfold_vars *our_variables,
    00169                                 int maxDistance1,
    00170                                 int maxDistance2));
    00171
    00172
    00173 #endif