Add missing doc files

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / 2Dpfold_8h_source.tex

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+\hypertarget{2Dpfold_8h}{\section{2\-Dpfold.h}
+\label{2Dpfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h}}
+}
+
+\begin{DoxyCode}
+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{DoxyCode}