-\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)}}
+\hypertarget{group__consensus__mfe__fold}{
+\section{MFE Consensus Structures for Sequence Alignment(s)}
+\label{group__consensus__mfe__fold}\index{MFE Consensus Structures for Sequence Alignment(s)@{MFE Consensus Structures for Sequence Alignment(s)}}
}
-Collaboration diagram for M\-F\-E Consensus Structures for Sequence Alignment(s)\-:
-\nopagebreak
+
+
+Collaboration diagram for MFE Consensus Structures for Sequence Alignment(s):\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__consensus__mfe__fold}
+\includegraphics[width=292pt]{group__consensus__mfe__fold}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item
float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure)
-\begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according consensus structure of an alignment of sequences. \end{DoxyCompactList}\item
+\begin{DoxyCompactList}\small\item\em Compute MFE and according consensus structure of an alignment of sequences. \item\end{DoxyCompactList}\item
float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\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}
-
+\begin{DoxyCompactList}\small\item\em Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \item\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}
-\subsection{Detailed Description}
+\begin{DoxyCompactList}\small\item\em Free the memory occupied by MFE alifold functions. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\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$$\ast$}]{strings, }
-\item[{char $\ast$}]{structure}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}
+\hypertarget{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{
+\index{consensus\_\-mfe\_\-fold@{consensus\_\-mfe\_\-fold}!alifold@{alifold}}
+\index{alifold@{alifold}!consensus_mfe_fold@{consensus\_\-mfe\_\-fold}}
+\subsubsection[{alifold}]{\setlength{\rightskip}{0pt plus 5cm}float alifold (const char $\ast$$\ast$ {\em strings}, \/ char $\ast$ {\em structure})}}
+\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'.
+Compute MFE 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}
+\item[{\em strings}]A pointer to a NULL terminated array of character arrays \item[{\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 MFE) \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$$\ast$}]{strings, }
-\item[{char $\ast$}]{structure}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}
-
-
-Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear.
+\hypertarget{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{
+\index{consensus\_\-mfe\_\-fold@{consensus\_\-mfe\_\-fold}!circalifold@{circalifold}}
+\index{circalifold@{circalifold}!consensus_mfe_fold@{consensus\_\-mfe\_\-fold}}
+\subsubsection[{circalifold}]{\setlength{\rightskip}{0pt plus 5cm}float circalifold (const char $\ast$$\ast$ {\em strings}, \/ char $\ast$ {\em structure})}}
+\label{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}
+Compute MFE 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}
+\item[{\em strings}]A pointer to a NULL terminated array of character arrays \item[{\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 MFE) \end{DoxyParams}
\begin{DoxyReturn}{Returns}
The free energy score in kcal/mol
\end{DoxyReturn}
git://source.jalview.org / jabaws.git / blobdiff