Add missing doc files

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / findpath_8h.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/findpath_8h.tex b/binaries/src/ViennaRNA/doc/latex/findpath_8h.tex
new file mode 100644 (file)
index 0000000..094bf87
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/latex/findpath_8h.tex
@@ -0,0 +1,103 @@
+\hypertarget{findpath_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/findpath.h File Reference}
+\label{findpath_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/findpath.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/findpath.\-h}}
+}
+
+
+Compute direct refolding paths between two secondary structures.  
+
+
+Include dependency graph for findpath.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{findpath_8h__incl}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+int \hyperlink{findpath_8h_ad0e14268e309af773ecd1fce6244ee50}{find\-\_\-saddle} (const char $\ast$seq, const char $\ast$struc1, const char $\ast$struc2, int max)
+\begin{DoxyCompactList}\small\item\em Find energy of a saddle point between 2 structures (serch only direct path) \end{DoxyCompactList}\item 
+\hyperlink{structpath__t}{path\-\_\-t} $\ast$ \hyperlink{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{get\-\_\-path} (const char $\ast$seq, const char $\ast$s1, const char $\ast$s2, int maxkeep)
+\begin{DoxyCompactList}\small\item\em Find refolding path between 2 structures (serch only direct path) \end{DoxyCompactList}\item 
+void \hyperlink{findpath_8h_a326e6d1640bbfd035e3869f5f4c188f7}{free\-\_\-path} (\hyperlink{structpath__t}{path\-\_\-t} $\ast$path)
+\begin{DoxyCompactList}\small\item\em Free memory allocated by \hyperlink{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{get\-\_\-path()} function. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Compute direct refolding paths between two secondary structures. 
+
+\subsection{Function Documentation}
+\hypertarget{findpath_8h_ad0e14268e309af773ecd1fce6244ee50}{\index{findpath.\-h@{findpath.\-h}!find\-\_\-saddle@{find\-\_\-saddle}}
+\index{find\-\_\-saddle@{find\-\_\-saddle}!findpath.h@{findpath.\-h}}
+\subsubsection[{find\-\_\-saddle}]{\setlength{\rightskip}{0pt plus 5cm}int find\-\_\-saddle (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{seq, }
+\item[{const char $\ast$}]{struc1, }
+\item[{const char $\ast$}]{struc2, }
+\item[{int}]{max}
+\end{DoxyParamCaption}
+)}}\label{findpath_8h_ad0e14268e309af773ecd1fce6244ee50}
+
+
+Find energy of a saddle point between 2 structures (serch only direct path) 
+
+
+\begin{DoxyParams}{Parameters}
+{\em seq} & R\-N\-A sequence \\
+\hline
+{\em struc1} & A pointer to the character array where the first secondary structure in dot-\/bracket notation will be written to \\
+\hline
+{\em struc2} & A pointer to the character array where the second secondary structure in dot-\/bracket notation will be written to \\
+\hline
+{\em max} & integer how many strutures are being kept during the search \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the saddle energy in 10cal/mol 
+\end{DoxyReturn}
+\hypertarget{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{\index{findpath.\-h@{findpath.\-h}!get\-\_\-path@{get\-\_\-path}}
+\index{get\-\_\-path@{get\-\_\-path}!findpath.h@{findpath.\-h}}
+\subsubsection[{get\-\_\-path}]{\setlength{\rightskip}{0pt plus 5cm}{\bf path\-\_\-t}$\ast$ get\-\_\-path (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{seq, }
+\item[{const char $\ast$}]{s1, }
+\item[{const char $\ast$}]{s2, }
+\item[{int}]{maxkeep}
+\end{DoxyParamCaption}
+)}}\label{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}
+
+
+Find refolding path between 2 structures (serch only direct path) 
+
+
+\begin{DoxyParams}{Parameters}
+{\em seq} & R\-N\-A sequence \\
+\hline
+{\em s1} & A pointer to the character array where the first secondary structure in dot-\/bracket notation will be written to \\
+\hline
+{\em s2} & A pointer to the character array where the second secondary structure in dot-\/bracket notation will be written to \\
+\hline
+{\em maxkeep} & integer how many strutures are being kept during the search \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+direct refolding path between two structures 
+\end{DoxyReturn}
+\hypertarget{findpath_8h_a326e6d1640bbfd035e3869f5f4c188f7}{\index{findpath.\-h@{findpath.\-h}!free\-\_\-path@{free\-\_\-path}}
+\index{free\-\_\-path@{free\-\_\-path}!findpath.h@{findpath.\-h}}
+\subsubsection[{free\-\_\-path}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-path (
+\begin{DoxyParamCaption}
+\item[{{\bf path\-\_\-t} $\ast$}]{path}
+\end{DoxyParamCaption}
+)}}\label{findpath_8h_a326e6d1640bbfd035e3869f5f4c188f7}
+
+
+Free memory allocated by \hyperlink{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{get\-\_\-path()} function. 
+
+
+\begin{DoxyParams}{Parameters}
+{\em path} & pointer to memory to be freed \\
+\hline
+\end{DoxyParams}