Add missing doc files

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

diff --git a/binaries/src/ViennaRNA/doc/latex/group__subopt__stochbt.tex b/binaries/src/ViennaRNA/doc/latex/group__subopt__stochbt.tex
new file mode 100644 (file)
index 0000000..93850a4
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/latex/group__subopt__stochbt.tex
@@ -0,0 +1,99 @@
+\hypertarget{group__subopt__stochbt}{\section{Stochastic backtracking in the Ensemble}
+\label{group__subopt__stochbt}\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
+}
+Collaboration diagram for Stochastic backtracking in the Ensemble\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__subopt__stochbt}
+\end{center}
+\end{figure}
+\subsection*{Modules}
+\begin{DoxyCompactItemize}
+\item 
+\hyperlink{group__consensus__stochbt}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}
+\item 
+\hyperlink{group__kl__neighborhood__stochbt}{Stochastic Backtracking of Structures from Distance Based Partitioning}
+\begin{DoxyCompactList}\small\item\em Contains functions related to stochastic backtracking from a specified distance class. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+char $\ast$ \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack} (char $\ast$sequence)
+\begin{DoxyCompactList}\small\item\em Sample a secondary structure from the Boltzmann ensemble according its probability\par
+. \end{DoxyCompactList}\item 
+char $\ast$ \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\-\_\-circ} (char $\ast$sequence)
+\begin{DoxyCompactList}\small\item\em Sample a secondary structure of a circular R\-N\-A from the Boltzmann ensemble according its probability. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item 
+int \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\-\_\-back}
+\begin{DoxyCompactList}\small\item\em Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+
+
+\subsection{Function Documentation}
+\hypertarget{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!pbacktrack@{pbacktrack}}
+\index{pbacktrack@{pbacktrack}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
+\subsubsection[{pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pbacktrack (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{sequence}
+\end{DoxyParamCaption}
+)}}\label{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}
+
+
+Sample a secondary structure from the Boltzmann ensemble according its probability\par
+. 
+
+\begin{DoxyPrecond}{Precondition}
+\hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\-\_\-fold\-\_\-par()} or \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} have to be called first to fill the partition function matrices
+\end{DoxyPrecond}
+
+\begin{DoxyParams}{Parameters}
+{\em sequence} & The R\-N\-A sequence \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+A sampled secondary structure in dot-\/bracket notation 
+\end{DoxyReturn}
+\hypertarget{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!pbacktrack\-\_\-circ@{pbacktrack\-\_\-circ}}
+\index{pbacktrack\-\_\-circ@{pbacktrack\-\_\-circ}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
+\subsubsection[{pbacktrack\-\_\-circ}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pbacktrack\-\_\-circ (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{sequence}
+\end{DoxyParamCaption}
+)}}\label{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}
+
+
+Sample a secondary structure of a circular R\-N\-A from the Boltzmann ensemble according its probability. 
+
+This function does the same as \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()} but assumes the R\-N\-A molecule to be circular
+
+\begin{DoxyPrecond}{Precondition}
+\hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\-\_\-fold\-\_\-par()} or pf\-\_\-fold\-\_\-circ() have to be called first to fill the partition function matrices
+\end{DoxyPrecond}
+
+\begin{DoxyParams}{Parameters}
+{\em sequence} & The R\-N\-A sequence \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+A sampled secondary structure in dot-\/bracket notation 
+\end{DoxyReturn}
+
+
+\subsection{Variable Documentation}
+\hypertarget{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!st\-\_\-back@{st\-\_\-back}}
+\index{st\-\_\-back@{st\-\_\-back}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
+\subsubsection[{st\-\_\-back}]{\setlength{\rightskip}{0pt plus 5cm}int st\-\_\-back}}\label{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}
+
+
+Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. 
+
+Set this variable to 1 prior to a call of \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} to ensure that all matrices needed for stochastic backtracking are filled in the forward recursions
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()}, \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\-\_\-circ} 
+\end{DoxySeeAlso}