\hypertarget{cofold_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_COFOLD\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_COFOLD\_H\_\_}
00003 \textcolor{preprocessor}{}
00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
00005 
00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
00011 \textcolor{preprocessor}{}
00065 \textcolor{keywordtype}{float} \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00066               \textcolor{keywordtype}{char} *structure);
00067 
00072 \textcolor{keywordtype}{float} \hyperlink{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{cofold_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00073                   \textcolor{keywordtype}{char} *structure,
00074                   \hyperlink{structparamT}{paramT} *parameters,
00075                   \textcolor{keywordtype}{int} is\_constrained);
00076 
00080 \textcolor{keywordtype}{void}      \hyperlink{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{free_co_arrays}(\textcolor{keywordtype}{void});
00081 
00085 \textcolor{keywordtype}{void}      \hyperlink{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{update_cofold_params}(\textcolor{keywordtype}{void});
00086 
00087 \textcolor{keywordtype}{void}      update\_cofold\_params\_par(\hyperlink{structparamT}{paramT} *parameters);
00088 
00089 
00105 \textcolor{keywordtype}{void} \hyperlink{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{export_cofold_arrays_gq}( \textcolor{keywordtype}{int} **f5\_p,
00106                               \textcolor{keywordtype}{int} **c\_p,
00107                               \textcolor{keywordtype}{int} **fML\_p,
00108                               \textcolor{keywordtype}{int} **fM1\_p,
00109                               \textcolor{keywordtype}{int} **fc\_p,
00110                               \textcolor{keywordtype}{int} **ggg\_p,
00111                               \textcolor{keywordtype}{int} **indx\_p,
00112                               \textcolor{keywordtype}{char} **ptype\_p);
00113 
00128 \textcolor{keywordtype}{void} \hyperlink{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{export_cofold_arrays}(\textcolor{keywordtype}{int} **f5\_p,
00129                           \textcolor{keywordtype}{int} **c\_p,
00130                           \textcolor{keywordtype}{int} **fML\_p,
00131                           \textcolor{keywordtype}{int} **fM1\_p,
00132                           \textcolor{keywordtype}{int} **fc\_p,
00133                           \textcolor{keywordtype}{int} **indx\_p,
00134                           \textcolor{keywordtype}{char} **ptype\_p);
00135 
00136 
00153 \hyperlink{structSOLUTION}{SOLUTION}  *\hyperlink{group__subopt__zuker_ga0d5104e3ecf119d8eabd40aa5fe47f90}{zukersubopt}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string});
00154 
00161 \hyperlink{structSOLUTION}{SOLUTION}  *\hyperlink{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}{zukersubopt_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00162                             \hyperlink{structparamT}{paramT} *parameters);
00163 
00172 \textcolor{keywordtype}{void} \hyperlink{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{get_monomere_mfes}( \textcolor{keywordtype}{float} *e1,
00173                         \textcolor{keywordtype}{float} *e2);
00174 
00175 
00180 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize_cofold}(\textcolor{keywordtype}{int} length));
00181 
00182 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
