RNAlib-2.0.7: H/2Dpfold.h Source 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 
00039 TwoDpfold_vars  *get_TwoDpfold_variables( const char *seq,
00040                                           const char *structure1,
00041                                           char *structure2,
00042                                           int circ);
00043 
00056 TwoDpfold_vars  *get_TwoDpfold_variables_from_MFE(TwoDfold_vars *mfe_vars);
00057 
00068 void            destroy_TwoDpfold_variables(TwoDpfold_vars *vars);
00069 
00075 DEPRECATED(FLT_OR_DBL          **TwoDpfold(TwoDpfold_vars *our_variables,
00076                                 int maxDistance1,
00077                                 int maxDistance2));
00078 
00084 DEPRECATED(FLT_OR_DBL          **TwoDpfold_circ(
00085                                 TwoDpfold_vars *our_variables,
00086                                 int maxDistance1,
00087                                 int maxDistance2));
00088 
00110 TwoDpfold_solution  *TwoDpfoldList( TwoDpfold_vars *vars,
00111                                     int maxDistance1,
00112                                     int maxDistance2);
00113 
00131 char            *TwoDpfold_pbacktrack(TwoDpfold_vars *vars,
00132                                       int d1,
00133                                       int d2);
00134 
00154 char            *TwoDpfold_pbacktrack5( TwoDpfold_vars *vars,
00155                                           int d1,
00156                                           int d2,
00157                                           unsigned int length);
00158 
00159 #endif