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

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+\hypertarget{group__centroid__fold}{\section{Compute the centroid structure}
+\label{group__centroid__fold}\index{Compute the centroid structure@{Compute the centroid structure}}
+}
+Collaboration diagram for Compute the centroid structure\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__centroid__fold}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+char $\ast$ \hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get\-\_\-centroid\-\_\-struct\-\_\-pl} (int length, double $\ast$dist, \hyperlink{structplist}{plist} $\ast$pl)
+\begin{DoxyCompactList}\small\item\em Get the centroid structure of the ensemble. \end{DoxyCompactList}\item 
+char $\ast$ \hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get\-\_\-centroid\-\_\-struct\-\_\-pr} (int length, double $\ast$dist, double $\ast$\hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr})
+\begin{DoxyCompactList}\small\item\em Get the centroid structure of the ensemble. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+
+
+\subsection{Function Documentation}
+\hypertarget{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{\index{Compute the centroid structure@{Compute the centroid structure}!get\-\_\-centroid\-\_\-struct\-\_\-pl@{get\-\_\-centroid\-\_\-struct\-\_\-pl}}
+\index{get\-\_\-centroid\-\_\-struct\-\_\-pl@{get\-\_\-centroid\-\_\-struct\-\_\-pl}!Compute the centroid structure@{Compute the centroid structure}}
+\subsubsection[{get\-\_\-centroid\-\_\-struct\-\_\-pl}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ get\-\_\-centroid\-\_\-struct\-\_\-pl (
+\begin{DoxyParamCaption}
+\item[{int}]{length, }
+\item[{double $\ast$}]{dist, }
+\item[{{\bf plist} $\ast$}]{pl}
+\end{DoxyParamCaption}
+)}}\label{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}
+
+
+Get the centroid structure of the ensemble. 
+
+This function is a threadsafe replacement for \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid()} with a 'plist' input
+
+The centroid is the structure with the minimal average distance to all other structures \par
+ $ <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} $ \par
+ Thus, the centroid is simply the structure containing all pairs with $p_ij>0.5$ The distance of the centroid to the ensemble is written to the memory adressed by {\itshape dist}.
+
+
+\begin{DoxyParams}[1]{Parameters}
+\mbox{\tt in}  & {\em length} & The length of the sequence \\
+\hline
+\mbox{\tt out}  & {\em dist} & A pointer to the distance variable where the centroid distance will be written to \\
+\hline
+\mbox{\tt in}  & {\em pl} & A pair list containing base pair probability information about the ensemble \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The centroid structure of the ensemble in dot-\/bracket notation 
+\end{DoxyReturn}
+\hypertarget{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{\index{Compute the centroid structure@{Compute the centroid structure}!get\-\_\-centroid\-\_\-struct\-\_\-pr@{get\-\_\-centroid\-\_\-struct\-\_\-pr}}
+\index{get\-\_\-centroid\-\_\-struct\-\_\-pr@{get\-\_\-centroid\-\_\-struct\-\_\-pr}!Compute the centroid structure@{Compute the centroid structure}}
+\subsubsection[{get\-\_\-centroid\-\_\-struct\-\_\-pr}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ get\-\_\-centroid\-\_\-struct\-\_\-pr (
+\begin{DoxyParamCaption}
+\item[{int}]{length, }
+\item[{double $\ast$}]{dist, }
+\item[{double $\ast$}]{pr}
+\end{DoxyParamCaption}
+)}}\label{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}
+
+
+Get the centroid structure of the ensemble. 
+
+This function is a threadsafe replacement for \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid()} with a probability array input
+
+The centroid is the structure with the minimal average distance to all other structures \par
+ $ <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} $ \par
+ Thus, the centroid is simply the structure containing all pairs with $p_ij>0.5$ The distance of the centroid to the ensemble is written to the memory adressed by {\itshape dist}.
+
+
+\begin{DoxyParams}[1]{Parameters}
+\mbox{\tt in}  & {\em length} & The length of the sequence \\
+\hline
+\mbox{\tt out}  & {\em dist} & A pointer to the distance variable where the centroid distance will be written to \\
+\hline
+\mbox{\tt in}  & {\em pr} & A upper triangular matrix containing base pair probabilities (access via iindx \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()} ) \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The centroid structure of the ensemble in dot-\/bracket notation 
+\end{DoxyReturn}