Add missing doc files

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / part__func__co_8h_source.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/part__func__co_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/part__func__co_8h_source.tex
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+\hypertarget{part__func__co_8h}{\section{part\-\_\-func\-\_\-co.\-h}
+\label{part__func__co_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.\-h}}
+}
+
+\begin{DoxyCode}
+00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_CO\_H\_\_}
+00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_CO\_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}{}
+00055 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}    \hyperlink{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{mirnatog};
+00056 
+00060 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{F\_monomer}[2];
+00061 
+00080 \hyperlink{structcofoldF}{cofoldF} \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\_pf\_fold}( \textcolor{keywordtype}{char} *sequence,
+00081                     \textcolor{keywordtype}{char} *structure);
+00082 
+00100 \hyperlink{structcofoldF}{cofoldF} \hyperlink{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{co\_pf\_fold\_par}( \textcolor{keywordtype}{char} *sequence,
+00101                         \textcolor{keywordtype}{char} *structure,
+00102                         \hyperlink{structpf__paramT}{pf\_paramT} *parameters,
+00103                         \textcolor{keywordtype}{int} calculate\_bppm,
+00104                         \textcolor{keywordtype}{int} is\_constrained);
+00105 
+00115 FLT\_OR\_DBL *\hyperlink{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c}{export\_co\_bppm}(\textcolor{keywordtype}{void});
+00116 
+00120 \textcolor{keywordtype}{void}    \hyperlink{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{free\_co\_pf\_arrays}(\textcolor{keywordtype}{void});
+00121 
+00136 \textcolor{keywordtype}{void}    \hyperlink{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{update\_co\_pf\_params}(\textcolor{keywordtype}{int} length);
+00137 
+00157 \textcolor{keywordtype}{void}    \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\_co\_pf\_params\_par}(\textcolor{keywordtype}{int} length,
+00158                                 \hyperlink{structpf__paramT}{pf\_paramT} *parameters);
+00159 
+00177 \textcolor{keywordtype}{void}    \hyperlink{group__pf__cofold_ga15ae04ac5ab84e876dcf0093120cb617}{compute\_probabilities}(\textcolor{keywordtype}{double} FAB,
+00178                               \textcolor{keywordtype}{double} FEA,
+00179                               \textcolor{keywordtype}{double} FEB,
+00180                               \textcolor{keyword}{struct} \hyperlink{structplist}{plist}  *prAB,
+00181                               \textcolor{keyword}{struct} \hyperlink{structplist}{plist}  *prA,
+00182                               \textcolor{keyword}{struct} \hyperlink{structplist}{plist}  *prB,
+00183                               \textcolor{keywordtype}{int} Alength);
+00184 
+00203 \hyperlink{structConcEnt}{ConcEnt} *\hyperlink{group__pf__cofold_ga5545cb936ac4ff93c7d699d46e72e8c7}{get\_concentrations}(\textcolor{keywordtype}{double} FEAB,
+00204                             \textcolor{keywordtype}{double} FEAA,
+00205                             \textcolor{keywordtype}{double} FEBB,
+00206                             \textcolor{keywordtype}{double} FEA,
+00207                             \textcolor{keywordtype}{double} FEB,
+00208                             \textcolor{keywordtype}{double} *startconc);
+00209 
+00210 
+00215 \textcolor{comment}{/*}
+00216 \textcolor{comment}{#################################################}
+00217 \textcolor{comment}{# DEPRECATED FUNCTIONS                          #}
+00218 \textcolor{comment}{#################################################}
+00219 \textcolor{comment}{*/}
+00220 
+00226 DEPRECATED(\hyperlink{structplist}{plist}  *\hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\_plist}( \textcolor{keyword}{struct} \hyperlink{structplist}{plist} *pl,
+00227                               \textcolor{keywordtype}{int} length,
+00228                               \textcolor{keywordtype}{double} cut\_off));
+00233 DEPRECATED(\textcolor{keywordtype}{void}   \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\_co\_pf\_fold}(\textcolor{keywordtype}{int} length));
+00234 
+00235 \textcolor{preprocessor}{#endif}
+\end{DoxyCode}