Add missing doc files

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

diff --git a/binaries/src/ViennaRNA/doc/latex/group__consensus__pf__fold.tex b/binaries/src/ViennaRNA/doc/latex/group__consensus__pf__fold.tex
new file mode 100644 (file)
index 0000000..bcd7b56
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/latex/group__consensus__pf__fold.tex
@@ -0,0 +1,127 @@
+\hypertarget{group__consensus__pf__fold}{\section{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
+\label{group__consensus__pf__fold}\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
+}
+Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s)\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__consensus__pf__fold}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+float \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\-\_\-fold\-\_\-par} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained, int is\-\_\-circular)
+\item 
+float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
+\begin{DoxyCompactList}\small\item\em The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\-\_\-info} structs. The list is terminated by the first entry with pi.\-i = 0. \end{DoxyCompactList}\item 
+float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
+\item 
+double $\ast$ \hyperlink{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{export\-\_\-ali\-\_\-bppm} (void)
+\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+
+
+\subsection{Function Documentation}
+\hypertarget{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-fold\-\_\-par@{alipf\-\_\-fold\-\_\-par}}
+\index{alipf\-\_\-fold\-\_\-par@{alipf\-\_\-fold\-\_\-par}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
+\subsubsection[{alipf\-\_\-fold\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-fold\-\_\-par (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$$\ast$}]{sequences, }
+\item[{char $\ast$}]{structure, }
+\item[{{\bf plist} $\ast$$\ast$}]{pl, }
+\item[{{\bf pf\-\_\-param\-T} $\ast$}]{parameters, }
+\item[{int}]{calculate\-\_\-bppm, }
+\item[{int}]{is\-\_\-constrained, }
+\item[{int}]{is\-\_\-circular}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}
+
+\begin{DoxyParams}{Parameters}
+{\em sequences} & \\
+\hline
+{\em structure} & \\
+\hline
+{\em pl} & \\
+\hline
+{\em parameters} & \\
+\hline
+{\em calculate\-\_\-bppm} & \\
+\hline
+{\em is\-\_\-constrained} & \\
+\hline
+{\em is\-\_\-circular} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-fold@{alipf\-\_\-fold}}
+\index{alipf\-\_\-fold@{alipf\-\_\-fold}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
+\subsubsection[{alipf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-fold (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$$\ast$}]{sequences, }
+\item[{char $\ast$}]{structure, }
+\item[{{\bf plist} $\ast$$\ast$}]{pl}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}
+
+
+The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\-\_\-info} structs. The list is terminated by the first entry with pi.\-i = 0. 
+
+
+\begin{DoxyParams}{Parameters}
+{\em sequences} & \\
+\hline
+{\em structure} & \\
+\hline
+{\em pl} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-circ\-\_\-fold@{alipf\-\_\-circ\-\_\-fold}}
+\index{alipf\-\_\-circ\-\_\-fold@{alipf\-\_\-circ\-\_\-fold}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
+\subsubsection[{alipf\-\_\-circ\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-circ\-\_\-fold (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$$\ast$}]{sequences, }
+\item[{char $\ast$}]{structure, }
+\item[{{\bf plist} $\ast$$\ast$}]{pl}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}
+
+\begin{DoxyParams}{Parameters}
+{\em sequences} & \\
+\hline
+{\em structure} & \\
+\hline
+{\em pl} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!export\-\_\-ali\-\_\-bppm@{export\-\_\-ali\-\_\-bppm}}
+\index{export\-\_\-ali\-\_\-bppm@{export\-\_\-ali\-\_\-bppm}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
+\subsubsection[{export\-\_\-ali\-\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ export\-\_\-ali\-\_\-bppm (
+\begin{DoxyParamCaption}
+\item[{void}]{}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}
+
+
+Get a pointer to the base pair probability array. 
+
+Accessing the base pair probabilities for a pair (i,j) is achieved by \begin{DoxyVerb}FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \end{DoxyVerb}
+
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()} 
+\end{DoxySeeAlso}
+\begin{DoxyReturn}{Returns}
+A pointer to the base pair probability array 
+\end{DoxyReturn}