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

   1 \hypertarget{2Dpfold_8h_source}{
   2 \section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h}
   3 }
   4
   5
   6 \begin{footnotesize}\begin{alltt}
   7 00001 \textcolor{comment}{/*}
   8 00002 \textcolor{comment}{      minimum free energy}
   9 00003 \textcolor{comment}{      RNA secondary structure with}
  10 00004 \textcolor{comment}{      basepair distance d to reference structure prediction}
  11 00005 \textcolor{comment}{}
  12 00006 \textcolor{comment}{*/}
  13 00007 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_}
  14 00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_}
  15 00009 \textcolor{preprocessor}{}
  16 00010 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
  17 00011
  18 00012 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
  19 00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
  20 00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
  21 00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
  22 00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  23 00017 \textcolor{preprocessor}{}
  24 00042 \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars}  *\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get_TwoDpfold_variables}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,
  25 00043                                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure1,
  26 00044                                           \textcolor{keywordtype}{char} *structure2,
  27 00045                                           \textcolor{keywordtype}{int} circ);
  28 00046
  29 00059 \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars}  *\hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get_TwoDpfold_variables_from_MFE}(\hyperlink{structTwoDfold__vars}{TwoDfold_vars} *mfe\_vars);
  30 00060
  31 00071 \textcolor{keywordtype}{void}            \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy_TwoDpfold_variables}(\hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *vars);
  32 00072
  33 00094 \hyperlink{structTwoDpfold__solution}{TwoDpfold_solution}  *\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList}( \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *vars,
  34 00095                                     \textcolor{keywordtype}{int} maxDistance1,
  35 00096                                     \textcolor{keywordtype}{int} maxDistance2);
  36 00097  \textcolor{comment}{/* End of group kl\_neighborhood\_pf */}
  37 00099
  38 00123 \textcolor{keywordtype}{char}            *\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold_pbacktrack}(\hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *vars,
  39 00124                                       \textcolor{keywordtype}{int} d1,
  40 00125                                       \textcolor{keywordtype}{int} d2);
  41 00126
  42 00146 \textcolor{keywordtype}{char}            *\hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{TwoDpfold_pbacktrack5}( \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *vars,
  43 00147                                           \textcolor{keywordtype}{int} d1,
  44 00148                                           \textcolor{keywordtype}{int} d2,
  45 00149                                           \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
  46 00150  \textcolor{comment}{/* End of group kl\_neighborhood\_stochbt */}
  47 00152
  48 00158 DEPRECATED(FLT\_OR\_DBL          **TwoDpfold(\hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *our\_variables,
  49 00159                                 \textcolor{keywordtype}{int} maxDistance1,
  50 00160                                 \textcolor{keywordtype}{int} maxDistance2));
  51 00161
  52 00167 DEPRECATED(FLT\_OR\_DBL          **TwoDpfold\_circ(
  53 00168                                 \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars} *our\_variables,
  54 00169                                 \textcolor{keywordtype}{int} maxDistance1,
  55 00170                                 \textcolor{keywordtype}{int} maxDistance2));
  56 00171
  57 00172
  58 00173 \textcolor{preprocessor}{#endif}
  59 \end{alltt}\end{footnotesize}