\hypertarget{ali__plex_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ali\_\-plex.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ALI\_PLEX\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ALI\_PLEX\_H\_\_}
00003 \textcolor{preprocessor}{}
00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
00008 \hyperlink{structduplexT}{duplexT}** aliLduplexfold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1[],
00009                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2[],
00010                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold,
00011                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} extension\_cost,
00012                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00013                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta,
00014                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fast,
00015                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_a,
00016                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_b,
00017                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_a,
00018                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_b);
00022 \hyperlink{structduplexT}{duplexT}** aliLduplexfold\_XS(\textcolor{keyword}{const} \textcolor{keywordtype}{char}* s1[],
00023                             \textcolor{keyword}{const} \textcolor{keywordtype}{char}* s2[],
00024                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
00025                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s2, 
00026                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold,
00027                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00028                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta,
00029                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} fast,
00030                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_a,
00031                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_b,
00032                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_a,
00033                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_b);
00034 
00035 \textcolor{comment}{/*}
00036 \textcolor{comment}{extern duplexT aliduplexfold(const char *s1[], const char *s2[], const int extens
      ion\_cost);}
00037 \textcolor{comment}{extern duplexT aliduplexfold\_XS(const char *s1[], const char *s2[],const int **ac
      cess\_s1, }
00038 \textcolor{comment}{const int **access\_s2, const int i\_pos, const int j\_pos, const int threshold);}
00039 \textcolor{comment}{*/}
00040 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
