\hypertarget{2Dpfold_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{comment}{/*}
00002 \textcolor{comment}{      minimum free energy}
00003 \textcolor{comment}{      RNA secondary structure with}
00004 \textcolor{comment}{      basepair distance d to reference structure prediction}
00005 \textcolor{comment}{}
00006 \textcolor{comment}{*/}
00007 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_}
00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_}
00009 \textcolor{preprocessor}{}
00010 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
00011 
00012 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
00017 \textcolor{preprocessor}{}
00042 \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars}  *\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get_TwoDpfold_variables}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,
00043                                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure1,
00044                                           \textcolor{keywordtype}{char} *structure2,
00045                                           \textcolor{keywordtype}{int} circ);
00046 
00059 \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars}  *\hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get_TwoDpfold_variables_from_MFE}(\hyperlink{structTwoDfold__vars}{TwoDfold_vars} *mfe\_vars);
00060 
00071 \textcolor{keywordtype}{void}            \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy_TwoDpfold_variables}(\hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *vars);
00072 
00094 \hyperlink{structTwoDpfold__solution}{TwoDpfold_solution}  *\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList}( \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *vars,
00095                                     \textcolor{keywordtype}{int} maxDistance1,
00096                                     \textcolor{keywordtype}{int} maxDistance2);
00097  \textcolor{comment}{/* End of group kl\_neighborhood\_pf */}
00099 
00123 \textcolor{keywordtype}{char}            *\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold_pbacktrack}(\hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *vars,
00124                                       \textcolor{keywordtype}{int} d1,
00125                                       \textcolor{keywordtype}{int} d2);
00126 
00146 \textcolor{keywordtype}{char}            *\hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{TwoDpfold_pbacktrack5}( \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *vars,
00147                                           \textcolor{keywordtype}{int} d1,
00148                                           \textcolor{keywordtype}{int} d2,
00149                                           \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
00150  \textcolor{comment}{/* End of group kl\_neighborhood\_stochbt */}
00152 
00158 DEPRECATED(FLT\_OR\_DBL          **TwoDpfold(\hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *our\_variables,
00159                                 \textcolor{keywordtype}{int} maxDistance1,
00160                                 \textcolor{keywordtype}{int} maxDistance2));
00161 
00167 DEPRECATED(FLT\_OR\_DBL          **TwoDpfold\_circ(
00168                                 \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *our\_variables,
00169                                 \textcolor{keywordtype}{int} maxDistance1,
00170                                 \textcolor{keywordtype}{int} maxDistance2));
00171 
00172 
00173 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
