binaries/src/ViennaRNA/doc/latex/2Dpfold_8h_source.tex

   1 \hypertarget{2Dpfold_8h}{\section{2\-Dpfold.h}
   2 \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}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{comment}{/*}
   7 00002 \textcolor{comment}{      minimum free energy}
   8 00003 \textcolor{comment}{      RNA secondary structure with}
   9 00004 \textcolor{comment}{      basepair distance d to reference structure prediction}
  10 00005 \textcolor{comment}{}
  11 00006 \textcolor{comment}{*/}
  12 00007 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_}
  13 00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_}
  14 00009 \textcolor{preprocessor}{}
  15 00010 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
  16 00011
  17 00012 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
  18 00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
  19 00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
  20 00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
  21 00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  22 00017 \textcolor{preprocessor}{}
  23 00042 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars}  *\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\_TwoDpfold\_variables}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,
  24 00043                                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure1,
  25 00044                                           \textcolor{keywordtype}{char} *structure2,
  26 00045                                           \textcolor{keywordtype}{int} circ);
  27 00046
  28 00059 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars}  *\hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\_TwoDpfold\_variables\_from\_MFE}(
  29       \hyperlink{structTwoDfold__vars}{TwoDfold\_vars} *mfe\_vars);
  30 00060
  31 00071 \textcolor{keywordtype}{void}            \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\_TwoDpfold\_variables}(
  32       \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars);
  33 00072
  34 00094 \hyperlink{structTwoDpfold__solution}{TwoDpfold\_solution}  *\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList}(
  35       \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars,
  36 00095                                     \textcolor{keywordtype}{int} maxDistance1,
  37 00096                                     \textcolor{keywordtype}{int} maxDistance2);
  38 00097  \textcolor{comment}{/* End of group kl\_neighborhood\_pf */}
  39 00099
  40 00123 \textcolor{keywordtype}{char}            *\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold\_pbacktrack}(\hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars,
  41 00124                                       \textcolor{keywordtype}{int} d1,
  42 00125                                       \textcolor{keywordtype}{int} d2);
  43 00126
  44 00146 \textcolor{keywordtype}{char}            *\hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{TwoDpfold\_pbacktrack5}( \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars,
  45 00147                                           \textcolor{keywordtype}{int} d1,
  46 00148                                           \textcolor{keywordtype}{int} d2,
  47 00149                                           \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
  48 00150  \textcolor{comment}{/* End of group kl\_neighborhood\_stochbt */}
  49 00152
  50 00158 DEPRECATED(FLT\_OR\_DBL          **TwoDpfold(\hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *our\_variables,
  51 00159                                 \textcolor{keywordtype}{int} maxDistance1,
  52 00160                                 \textcolor{keywordtype}{int} maxDistance2));
  53 00161
  54 00167 DEPRECATED(FLT\_OR\_DBL          **TwoDpfold\_circ(
  55 00168                                 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *our\_variables,
  56 00169                                 \textcolor{keywordtype}{int} maxDistance1,
  57 00170                                 \textcolor{keywordtype}{int} maxDistance2));
  58 00171
  59 00172
  60 00173 \textcolor{preprocessor}{#endif}
  61 \end{DoxyCode}