-\hypertarget{group__local__pf__fold}{\section{Partition functions for locally stable secondary structures}
+\hypertarget{group__local__pf__fold}{
+\section{Partition functions for locally stable secondary structures}
\label{group__local__pf__fold}\index{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}}
}
-Collaboration diagram for Partition functions for locally stable secondary structures\-:
-\nopagebreak
+
+
+Collaboration diagram for Partition functions for locally stable secondary structures:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__local__pf__fold}
+\includegraphics[width=306pt]{group__local__pf__fold}
\end{center}
\end{figure}
-\subsection*{Files}
-\begin{DoxyCompactItemize}
-\item
-file \hyperlink{LPfold_8h}{L\-Pfold.\-h}
-\begin{DoxyCompactList}\small\item\em Function declarations of partition function variants of the Lfold algorithm. \end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item
-void \hyperlink{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}{update\-\_\-pf\-\_\-params\-L\-P} (int length)
+void \hyperlink{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}{update\_\-pf\_\-paramsLP} (int length)
\item
-\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{pfl\-\_\-fold} (char $\ast$sequence, int win\-Size, int pair\-Size, float cutoffb, double $\ast$$\ast$p\-U, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, F\-I\-L\-E $\ast$p\-Ufp, F\-I\-L\-E $\ast$spup)
-\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \end{DoxyCompactList}\item
-\hypertarget{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{pfl\-\_\-fold\-\_\-par} (char $\ast$sequence, int win\-Size, int pair\-Size, float cutoffb, double $\ast$$\ast$p\-U, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, F\-I\-L\-E $\ast$p\-Ufp, F\-I\-L\-E $\ast$spup, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters)}\label{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}
-
-\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \end{DoxyCompactList}\item
-void \hyperlink{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}{putoutp\-U\-\_\-prob} (double $\ast$$\ast$p\-U, int length, int ulength, F\-I\-L\-E $\ast$fp, int energies)
-\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (p\-U) or opening energies into a file. \end{DoxyCompactList}\item
-void \hyperlink{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}{putoutp\-U\-\_\-prob\-\_\-bin} (double $\ast$$\ast$p\-U, int length, int ulength, F\-I\-L\-E $\ast$fp, int energies)
-\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (p\-U) or opening energies into a binary file. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{pfl\_\-fold} (char $\ast$sequence, int winSize, int pairSize, float cutoffb, double $\ast$$\ast$pU, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, FILE $\ast$pUfp, FILE $\ast$spup)
+\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \item\end{DoxyCompactList}\item
+\hypertarget{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{
+\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{pfl\_\-fold\_\-par} (char $\ast$sequence, int winSize, int pairSize, float cutoffb, double $\ast$$\ast$pU, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, FILE $\ast$pUfp, FILE $\ast$spup, \hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$parameters)}
+\label{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}
-
-\subsection{Detailed Description}
+\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \item\end{DoxyCompactList}\item
+void \hyperlink{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}{putoutpU\_\-prob} (double $\ast$$\ast$pU, int length, int ulength, FILE $\ast$fp, int energies)
+\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (pU) or opening energies into a file. \item\end{DoxyCompactList}\item
+void \hyperlink{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}{putoutpU\_\-prob\_\-bin} (double $\ast$$\ast$pU, int length, int ulength, FILE $\ast$fp, int energies)
+\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (pU) or opening energies into a binary file. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection{Function Documentation}
-\hypertarget{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}{\index{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!update\-\_\-pf\-\_\-params\-L\-P@{update\-\_\-pf\-\_\-params\-L\-P}}
-\index{update\-\_\-pf\-\_\-params\-L\-P@{update\-\_\-pf\-\_\-params\-L\-P}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}}
-\subsubsection[{update\-\_\-pf\-\_\-params\-L\-P}]{\setlength{\rightskip}{0pt plus 5cm}void update\-\_\-pf\-\_\-params\-L\-P (
-\begin{DoxyParamCaption}
-\item[{int}]{length}
-\end{DoxyParamCaption}
-)}}\label{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}
+\hypertarget{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}{
+\index{local\_\-pf\_\-fold@{local\_\-pf\_\-fold}!update\_\-pf\_\-paramsLP@{update\_\-pf\_\-paramsLP}}
+\index{update\_\-pf\_\-paramsLP@{update\_\-pf\_\-paramsLP}!local_pf_fold@{local\_\-pf\_\-fold}}
+\subsubsection[{update\_\-pf\_\-paramsLP}]{\setlength{\rightskip}{0pt plus 5cm}void update\_\-pf\_\-paramsLP (int {\em length})}}
+\label{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}
\begin{DoxyParams}{Parameters}
-{\em length} & \\
-\hline
-\end{DoxyParams}
-\hypertarget{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{\index{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!pfl\-\_\-fold@{pfl\-\_\-fold}}
-\index{pfl\-\_\-fold@{pfl\-\_\-fold}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}}
-\subsubsection[{pfl\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}{\bf plist}$\ast$ pfl\-\_\-fold (
-\begin{DoxyParamCaption}
-\item[{char $\ast$}]{sequence, }
-\item[{int}]{win\-Size, }
-\item[{int}]{pair\-Size, }
-\item[{float}]{cutoffb, }
-\item[{double $\ast$$\ast$}]{p\-U, }
-\item[{struct {\bf plist} $\ast$$\ast$}]{dpp2, }
-\item[{F\-I\-L\-E $\ast$}]{p\-Ufp, }
-\item[{F\-I\-L\-E $\ast$}]{spup}
-\end{DoxyParamCaption}
-)}}\label{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}
-
+\item[{\em length}]\end{DoxyParams}
+\hypertarget{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{
+\index{local\_\-pf\_\-fold@{local\_\-pf\_\-fold}!pfl\_\-fold@{pfl\_\-fold}}
+\index{pfl\_\-fold@{pfl\_\-fold}!local_pf_fold@{local\_\-pf\_\-fold}}
+\subsubsection[{pfl\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}{\bf plist}$\ast$ pfl\_\-fold (char $\ast$ {\em sequence}, \/ int {\em winSize}, \/ int {\em pairSize}, \/ float {\em cutoffb}, \/ double $\ast$$\ast$ {\em pU}, \/ struct {\bf plist} $\ast$$\ast$ {\em dpp2}, \/ FILE $\ast$ {\em pUfp}, \/ FILE $\ast$ {\em spup})}}
+\label{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}
-Compute partition functions for locally stable secondary structures.
-pfl\-\_\-fold computes partition functions for every window of size 'win\-Size' possible in a R\-N\-A molecule, allowing only pairs with a span smaller than 'pair\-Size'. It returns the mean pair probabilities averaged over all windows containing the pair in 'pl'. 'win\-Size' should always be $>$= 'pair\-Size'. Note that in contrast to \hyperlink{group__local__mfe__fold_ga16e5a70e60835bb969eaecbe6482f1be}{Lfold()}, bases outside of the window do not influence the structure at all. Only probabilities higher than 'cutoffb' are kept.
+Compute partition functions for locally stable secondary structures. pfl\_\-fold computes partition functions for every window of size 'winSize' possible in a RNA molecule, allowing only pairs with a span smaller than 'pairSize'. It returns the mean pair probabilities averaged over all windows containing the pair in 'pl'. 'winSize' should always be $>$= 'pairSize'. Note that in contrast to \hyperlink{group__local__mfe__fold_ga16e5a70e60835bb969eaecbe6482f1be}{Lfold()}, bases outside of the window do not influence the structure at all. Only probabilities higher than 'cutoffb' are kept.
-If 'p\-U' is supplied (i.\-e is not the N\-U\-L\-L pointer), \hyperlink{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{pfl\-\_\-fold()} will also compute the mean probability that regions of length 'u' and smaller are unpaired. The parameter 'u' is supplied in 'pup\mbox{[}0\mbox{]}\mbox{[}0\mbox{]}'. On return the 'pup' array will contain these probabilities, with the entry on 'pup\mbox{[}x\mbox{]}\mbox{[}y\mbox{]}' containing the mean probability that x and the y-\/1 preceding bases are unpaired. The 'p\-U' array needs to be large enough to hold n+1 float$\ast$ entries, where n is the sequence length.
+If 'pU' is supplied (i.e is not the NULL pointer), \hyperlink{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{pfl\_\-fold()} will also compute the mean probability that regions of length 'u' and smaller are unpaired. The parameter 'u' is supplied in 'pup\mbox{[}0\mbox{]}\mbox{[}0\mbox{]}'. On return the 'pup' array will contain these probabilities, with the entry on 'pup\mbox{[}x\mbox{]}\mbox{[}y\mbox{]}' containing the mean probability that x and the y-\/1 preceding bases are unpaired. The 'pU' array needs to be large enough to hold n+1 float$\ast$ entries, where n is the sequence length.
-If an array dpp2 is supplied, the probability of base pair (i,j) given that there already exists a base pair (i+1,j-\/1) is also computed and saved in this array. If p\-Ufp is given (i.\-e. not N\-U\-L\-L), p\-U is not saved but put out imediately. If spup is given (i.\-e. is not N\-U\-L\-L), the pair probabilities in pl are not saved but put out imediately.
+If an array dpp2 is supplied, the probability of base pair (i,j) given that there already exists a base pair (i+1,j-\/1) is also computed and saved in this array. If pUfp is given (i.e. not NULL), pU is not saved but put out imediately. If spup is given (i.e. is not NULL), the pair probabilities in pl are not saved but put out imediately.
\begin{DoxyParams}{Parameters}
-{\em sequence} & R\-N\-A sequence \\
-\hline
-{\em win\-Size} & size of the window \\
-\hline
-{\em pair\-Size} & maximum size of base pair \\
-\hline
-{\em cutoffb} & cutoffb for base pairs \\
-\hline
-{\em p\-U} & array holding all unpaired probabilities \\
-\hline
-{\em dpp2} & array of dependent pair probabilities \\
-\hline
-{\em p\-Ufp} & file pointer for p\-U \\
-\hline
-{\em spup} & file pointer for pair probabilities \\
-\hline
-\end{DoxyParams}
+\item[{\em sequence}]RNA sequence \item[{\em winSize}]size of the window \item[{\em pairSize}]maximum size of base pair \item[{\em cutoffb}]cutoffb for base pairs \item[{\em pU}]array holding all unpaired probabilities \item[{\em dpp2}]array of dependent pair probabilities \item[{\em pUfp}]file pointer for pU \item[{\em spup}]file pointer for pair probabilities \end{DoxyParams}
\begin{DoxyReturn}{Returns}
list of pair probabilities
\end{DoxyReturn}
-\hypertarget{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}{\index{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!putoutp\-U\-\_\-prob@{putoutp\-U\-\_\-prob}}
-\index{putoutp\-U\-\_\-prob@{putoutp\-U\-\_\-prob}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}}
-\subsubsection[{putoutp\-U\-\_\-prob}]{\setlength{\rightskip}{0pt plus 5cm}void putoutp\-U\-\_\-prob (
-\begin{DoxyParamCaption}
-\item[{double $\ast$$\ast$}]{p\-U, }
-\item[{int}]{length, }
-\item[{int}]{ulength, }
-\item[{F\-I\-L\-E $\ast$}]{fp, }
-\item[{int}]{energies}
-\end{DoxyParamCaption}
-)}}\label{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}
-
+\hypertarget{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}{
+\index{local\_\-pf\_\-fold@{local\_\-pf\_\-fold}!putoutpU\_\-prob@{putoutpU\_\-prob}}
+\index{putoutpU\_\-prob@{putoutpU\_\-prob}!local_pf_fold@{local\_\-pf\_\-fold}}
+\subsubsection[{putoutpU\_\-prob}]{\setlength{\rightskip}{0pt plus 5cm}void putoutpU\_\-prob (double $\ast$$\ast$ {\em pU}, \/ int {\em length}, \/ int {\em ulength}, \/ FILE $\ast$ {\em fp}, \/ int {\em energies})}}
+\label{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}
-Writes the unpaired probabilities (p\-U) or opening energies into a file.
-Can write either the unpaired probabilities (accessibilities) p\-U or the opening energies -\/log(p\-U)k\-T into a file
+Writes the unpaired probabilities (pU) or opening energies into a file. Can write either the unpaired probabilities (accessibilities) pU or the opening energies -\/log(pU)kT into a file
\begin{DoxyParams}{Parameters}
-{\em p\-U} & pair probabilities \\
-\hline
-{\em length} & length of R\-N\-A sequence \\
-\hline
-{\em ulength} & maximum length of unpaired stretch \\
-\hline
-{\em fp} & file pointer of destination file \\
-\hline
-{\em energies} & switch to put out as opening energies \\
-\hline
-\end{DoxyParams}
-\hypertarget{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}{\index{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!putoutp\-U\-\_\-prob\-\_\-bin@{putoutp\-U\-\_\-prob\-\_\-bin}}
-\index{putoutp\-U\-\_\-prob\-\_\-bin@{putoutp\-U\-\_\-prob\-\_\-bin}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}}
-\subsubsection[{putoutp\-U\-\_\-prob\-\_\-bin}]{\setlength{\rightskip}{0pt plus 5cm}void putoutp\-U\-\_\-prob\-\_\-bin (
-\begin{DoxyParamCaption}
-\item[{double $\ast$$\ast$}]{p\-U, }
-\item[{int}]{length, }
-\item[{int}]{ulength, }
-\item[{F\-I\-L\-E $\ast$}]{fp, }
-\item[{int}]{energies}
-\end{DoxyParamCaption}
-)}}\label{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}
-
-
-Writes the unpaired probabilities (p\-U) or opening energies into a binary file.
-
-Can write either the unpaired probabilities (accessibilities) p\-U or the opening energies -\/log(p\-U)k\-T into a file
+\item[{\em pU}]pair probabilities \item[{\em length}]length of RNA sequence \item[{\em ulength}]maximum length of unpaired stretch \item[{\em fp}]file pointer of destination file \item[{\em energies}]switch to put out as opening energies \end{DoxyParams}
+\hypertarget{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}{
+\index{local\_\-pf\_\-fold@{local\_\-pf\_\-fold}!putoutpU\_\-prob\_\-bin@{putoutpU\_\-prob\_\-bin}}
+\index{putoutpU\_\-prob\_\-bin@{putoutpU\_\-prob\_\-bin}!local_pf_fold@{local\_\-pf\_\-fold}}
+\subsubsection[{putoutpU\_\-prob\_\-bin}]{\setlength{\rightskip}{0pt plus 5cm}void putoutpU\_\-prob\_\-bin (double $\ast$$\ast$ {\em pU}, \/ int {\em length}, \/ int {\em ulength}, \/ FILE $\ast$ {\em fp}, \/ int {\em energies})}}
+\label{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}
+
+
+Writes the unpaired probabilities (pU) or opening energies into a binary file. Can write either the unpaired probabilities (accessibilities) pU or the opening energies -\/log(pU)kT into a file
\begin{DoxyParams}{Parameters}
-{\em p\-U} & pair probabilities \\
-\hline
-{\em length} & length of R\-N\-A sequence \\
-\hline
-{\em ulength} & maximum length of unpaired stretch \\
-\hline
-{\em fp} & file pointer of destination file \\
-\hline
-{\em energies} & switch to put out as opening energies \\
-\hline
-\end{DoxyParams}
+\item[{\em pU}]pair probabilities \item[{\em length}]length of RNA sequence \item[{\em ulength}]maximum length of unpaired stretch \item[{\em fp}]file pointer of destination file \item[{\em energies}]switch to put out as opening energies \end{DoxyParams}
git://source.jalview.org / jabaws.git / blobdiff