-\hypertarget{group__centroid__fold}{\section{Compute the centroid structure}
+\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
+
+
+Collaboration diagram for Compute the centroid structure:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__centroid__fold}
+\includegraphics[width=241pt]{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}
+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. \item\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. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\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}
-
+\hypertarget{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{
+\index{centroid\_\-fold@{centroid\_\-fold}!get\_\-centroid\_\-struct\_\-pl@{get\_\-centroid\_\-struct\_\-pl}}
+\index{get\_\-centroid\_\-struct\_\-pl@{get\_\-centroid\_\-struct\_\-pl}!centroid_fold@{centroid\_\-fold}}
+\subsubsection[{get\_\-centroid\_\-struct\_\-pl}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ get\_\-centroid\_\-struct\_\-pl (int {\em length}, \/ double $\ast$ {\em dist}, \/ {\bf plist} $\ast$ {\em pl})}}
+\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
+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}.
+ 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{DoxyParams}{Parameters}
+\item[\mbox{$\leftarrow$} {\em length}]The length of the sequence \item[\mbox{$\rightarrow$} {\em dist}]A pointer to the distance variable where the centroid distance will be written to \item[\mbox{$\leftarrow$} {\em pl}]A pair list containing base pair probability information about the ensemble \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}
-
+\hypertarget{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{
+\index{centroid\_\-fold@{centroid\_\-fold}!get\_\-centroid\_\-struct\_\-pr@{get\_\-centroid\_\-struct\_\-pr}}
+\index{get\_\-centroid\_\-struct\_\-pr@{get\_\-centroid\_\-struct\_\-pr}!centroid_fold@{centroid\_\-fold}}
+\subsubsection[{get\_\-centroid\_\-struct\_\-pr}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ get\_\-centroid\_\-struct\_\-pr (int {\em length}, \/ double $\ast$ {\em dist}, \/ double $\ast$ {\em pr})}}
+\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
+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}.
+ 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{DoxyParams}{Parameters}
+\item[\mbox{$\leftarrow$} {\em length}]The length of the sequence \item[\mbox{$\rightarrow$} {\em dist}]A pointer to the distance variable where the centroid distance will be written to \item[\mbox{$\leftarrow$} {\em pr}]A upper triangular matrix containing base pair probabilities (access via iindx \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_\-iindx()} ) \end{DoxyParams}
\begin{DoxyReturn}{Returns}
The centroid structure of the ensemble in dot-\/bracket notation
\end{DoxyReturn}
git://source.jalview.org / jabaws.git / blobdiff