-\hypertarget{group__subopt__stochbt}{\section{Stochastic backtracking in the Ensemble}
+\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
+
+
+Collaboration diagram for Stochastic backtracking in the Ensemble:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__subopt__stochbt}
+\includegraphics[width=420pt]{group__subopt__stochbt}
\end{center}
\end{figure}
\subsection*{Modules}
\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}
+
+
+\begin{DoxyCompactList}\small\item\em Contains functions related to stochastic backtracking from a specified distance class. \item\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}
+. \item\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 RNA from the Boltzmann ensemble according its probability. \item\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}
+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. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\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}
+\hypertarget{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{
+\index{subopt\_\-stochbt@{subopt\_\-stochbt}!pbacktrack@{pbacktrack}}
+\index{pbacktrack@{pbacktrack}!subopt_stochbt@{subopt\_\-stochbt}}
+\subsubsection[{pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pbacktrack (char $\ast$ {\em sequence})}}
+\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
+. \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}
+\item[{\em sequence}]The RNA sequence \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}
+\hypertarget{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{
+\index{subopt\_\-stochbt@{subopt\_\-stochbt}!pbacktrack\_\-circ@{pbacktrack\_\-circ}}
+\index{pbacktrack\_\-circ@{pbacktrack\_\-circ}!subopt_stochbt@{subopt\_\-stochbt}}
+\subsubsection[{pbacktrack\_\-circ}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pbacktrack\_\-circ (char $\ast$ {\em sequence})}}
+\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
+Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. This function does the same as \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()} but assumes the RNA 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
+\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}
+\item[{\em sequence}]The RNA sequence \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}
-
+\hypertarget{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{
+\index{subopt\_\-stochbt@{subopt\_\-stochbt}!st\_\-back@{st\_\-back}}
+\index{st\_\-back@{st\_\-back}!subopt_stochbt@{subopt\_\-stochbt}}
+\subsubsection[{st\_\-back}]{\setlength{\rightskip}{0pt plus 5cm}int {\bf 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
+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}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()}, \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\_\-circ}
\end{DoxySeeAlso}
git://source.jalview.org / jabaws.git / blobdiff