\hypertarget{plex_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plex.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_PLEX\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PLEX\_H\_\_}
00003 \textcolor{preprocessor}{}
00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
00005 
00006 
00007 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{subopt_sorted};
00008 
00012 \hyperlink{structduplexT}{duplexT}** Lduplexfold(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00013                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
00014                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold,
00015                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} extension\_cost,
00016                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00017                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta,
00018                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} fast,
00019                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_a,
00020                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_b,
00021                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_a,
00022                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_b);
00023 
00027 \hyperlink{structduplexT}{duplexT}** Lduplexfold\_XS( \textcolor{keyword}{const} \textcolor{keywordtype}{char}*s1,
00028                           \textcolor{keyword}{const} \textcolor{keywordtype}{char}* s2,
00029                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
00030                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s2,
00031                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold,
00032                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta,
00033                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00034                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fast,
00035                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_a,
00036                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_b,
00037                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_a,
00038                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_b);\textcolor{comment}{/* , const int target\_dead, const int qu
      ery\_dead); */}
00039 
00043 \hyperlink{structduplexT}{duplexT}** Lduplexfold\_C(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00044                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
00045                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold,
00046                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} extension\_cost,
00047                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00048                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta,
00049                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} fast,
00050                         \textcolor{keyword}{const} \textcolor{keywordtype}{char}* structure,
00051                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_a,
00052                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_b,
00053                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_a,
00054                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_b);
00055 
00060 \hyperlink{structduplexT}{duplexT}** Lduplexfold\_CXS(\textcolor{keyword}{const} \textcolor{keywordtype}{char}*s1,
00061                           \textcolor{keyword}{const} \textcolor{keywordtype}{char}* s2,
00062                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
00063                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s2,
00064                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold,
00065                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta,
00066                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00067                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fast,
00068                           \textcolor{keyword}{const} \textcolor{keywordtype}{char}* structure,
00069                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_a,
00070                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_b,
00071                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_a,
00072                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_b); \textcolor{comment}{/*, const int target\_dead, const int qu
      ery\_dead); */}
00073 
00074 
00075 
00076 
00077 \textcolor{keywordtype}{int}      arraySize(\hyperlink{structduplexT}{duplexT}** array);
00078 \textcolor{keywordtype}{void}     freeDuplexT(\hyperlink{structduplexT}{duplexT}** array);
00079 
00080 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
