Add missing doc files

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / cofold_8h_source.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/cofold_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/cofold_8h_source.tex
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+\hypertarget{cofold_8h}{\section{cofold.\-h}
+\label{cofold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.\-h}}
+}
+
+\begin{DoxyCode}
+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{DoxyCode}