Add missing doc files

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

diff --git a/binaries/src/ViennaRNA/doc/latex/group__consensus__mfe__fold.tex b/binaries/src/ViennaRNA/doc/latex/group__consensus__mfe__fold.tex
new file mode 100644 (file)
index 0000000..6887801
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/latex/group__consensus__mfe__fold.tex
@@ -0,0 +1,75 @@
+\hypertarget{group__consensus__mfe__fold}{\section{M\-F\-E Consensus Structures for Sequence Alignment(s)}
+\label{group__consensus__mfe__fold}\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
+}
+Collaboration diagram for M\-F\-E Consensus Structures for Sequence Alignment(s)\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__consensus__mfe__fold}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according consensus structure of an alignment of sequences. \end{DoxyCompactList}\item 
+float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\ast$strings, char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \end{DoxyCompactList}\item 
+\hypertarget{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{void \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\-\_\-alifold\-\_\-arrays} (void)}\label{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}
+
+\begin{DoxyCompactList}\small\item\em Free the memory occupied by M\-F\-E alifold functions. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+
+
+\subsection{Function Documentation}
+\hypertarget{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}!alifold@{alifold}}
+\index{alifold@{alifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
+\subsubsection[{alifold}]{\setlength{\rightskip}{0pt plus 5cm}float alifold (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$$\ast$}]{strings, }
+\item[{char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}
+
+
+Compute M\-F\-E and according consensus structure of an alignment of sequences. 
+
+This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.
+
+Sufficient space must be allocated for 'structure' before calling \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()}.
+
+
+\begin{DoxyParams}{Parameters}
+{\em strings} & A pointer to a N\-U\-L\-L terminated array of character arrays \\
+\hline
+{\em structure} & A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the M\-F\-E) \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The free energy score in kcal/mol 
+\end{DoxyReturn}
+\hypertarget{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}!circalifold@{circalifold}}
+\index{circalifold@{circalifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
+\subsubsection[{circalifold}]{\setlength{\rightskip}{0pt plus 5cm}float circalifold (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$$\ast$}]{strings, }
+\item[{char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}
+
+
+Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear. 
+
+
+\begin{DoxyParams}{Parameters}
+{\em strings} & A pointer to a N\-U\-L\-L terminated array of character arrays \\
+\hline
+{\em structure} & A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the M\-F\-E) \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The free energy score in kcal/mol 
+\end{DoxyReturn}