X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2FViennaRNA%2Fdoc%2Flatex%2Fgroup__subopt__wuchty.tex;h=f959b8c0393ab698022b4dd0ee15d2a2a89a180e;hb=ecfc686151bf027d4deb3c7a7510861d35c51730;hp=1269e232d8314ddc1198b7a0e3f089f5851c10d5;hpb=b4ff3ef8dc5d197f41d83de832e94e3b45a5c12e;p=jabaws.git

diff --git a/binaries/src/ViennaRNA/doc/latex/group__subopt__wuchty.tex b/binaries/src/ViennaRNA/doc/latex/group__subopt__wuchty.tex
index 1269e23..f959b8c 100644
--- a/binaries/src/ViennaRNA/doc/latex/group__subopt__wuchty.tex
+++ b/binaries/src/ViennaRNA/doc/latex/group__subopt__wuchty.tex
@@ -1,96 +1,71 @@
-\hypertarget{group__subopt__wuchty}{\section{Suboptimal structures within an energy band arround the M\-F\-E}
-\label{group__subopt__wuchty}\index{Suboptimal structures within an energy band arround the M\-F\-E@{Suboptimal structures within an energy band arround the M\-F\-E}}
+\hypertarget{group__subopt__wuchty}{
+\section{Suboptimal structures within an energy band arround the MFE}
+\label{group__subopt__wuchty}\index{Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the MFE}}
 }
-Collaboration diagram for Suboptimal structures within an energy band arround the M\-F\-E\-:
-\nopagebreak
+
+
+Collaboration diagram for Suboptimal structures within an energy band arround the MFE:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=348pt]{group__subopt__wuchty}
+\includegraphics[width=272pt]{group__subopt__wuchty}
 \end{center}
 \end{figure}
 \subsection*{Functions}
 \begin{DoxyCompactItemize}
 \item 
-\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt} (char $\ast$seq, char $\ast$structure, int delta, F\-I\-L\-E $\ast$fp)
-\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \end{DoxyCompactList}\item 
-\hypertarget{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\-\_\-par} (char $\ast$seq, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int delta, int is\-\_\-constrained, int is\-\_\-circular, F\-I\-L\-E $\ast$fp)}\label{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}
-
-\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \end{DoxyCompactList}\item 
-\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\-\_\-circ} (char $\ast$seq, char $\ast$sequence, int delta, F\-I\-L\-E $\ast$fp)
-\begin{DoxyCompactList}\small\item\em Returns list of circular subopt structures or writes to fp. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt} (char $\ast$seq, char $\ast$structure, int delta, FILE $\ast$fp)
+\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \item\end{DoxyCompactList}\item 
+\hypertarget{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{
+\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\_\-par} (char $\ast$seq, char $\ast$structure, \hyperlink{structparamT}{paramT} $\ast$parameters, int delta, int is\_\-constrained, int is\_\-circular, FILE $\ast$fp)}
+\label{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}
+
+\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \item\end{DoxyCompactList}\item 
+\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\_\-circ} (char $\ast$seq, char $\ast$sequence, int delta, FILE $\ast$fp)
+\begin{DoxyCompactList}\small\item\em Returns list of circular subopt structures or writes to fp. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
 \subsection*{Variables}
 \begin{DoxyCompactItemize}
 \item 
-\hypertarget{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{int \hyperlink{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{subopt\-\_\-sorted}}\label{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}
-
-\begin{DoxyCompactList}\small\item\em Sort output by energy. \end{DoxyCompactList}\item 
-\hypertarget{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{double \hyperlink{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{print\-\_\-energy}}\label{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}
+\hypertarget{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{
+int \hyperlink{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{subopt\_\-sorted}}
+\label{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}
 
-\begin{DoxyCompactList}\small\item\em printing threshold for use with log\-M\-L \end{DoxyCompactList}\end{DoxyCompactItemize}
+\begin{DoxyCompactList}\small\item\em Sort output by energy. \item\end{DoxyCompactList}\item 
+\hypertarget{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{
+double \hyperlink{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{print\_\-energy}}
+\label{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}
 
-
-\subsection{Detailed Description}
+\begin{DoxyCompactList}\small\item\em printing threshold for use with logML \item\end{DoxyCompactList}\end{DoxyCompactItemize}
 
 
 \subsection{Function Documentation}
-\hypertarget{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{\index{Suboptimal structures within an energy band arround the M\-F\-E@{Suboptimal structures within an energy band arround the M\-F\-E}!subopt@{subopt}}
-\index{subopt@{subopt}!Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the M\-F\-E}}
-\subsubsection[{subopt}]{\setlength{\rightskip}{0pt plus 5cm}{\bf S\-O\-L\-U\-T\-I\-O\-N}$\ast$ subopt (
-\begin{DoxyParamCaption}
-\item[{char $\ast$}]{seq, }
-\item[{char $\ast$}]{structure, }
-\item[{int}]{delta, }
-\item[{F\-I\-L\-E $\ast$}]{fp}
-\end{DoxyParamCaption}
-)}}\label{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}
-
+\hypertarget{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{
+\index{subopt\_\-wuchty@{subopt\_\-wuchty}!subopt@{subopt}}
+\index{subopt@{subopt}!subopt_wuchty@{subopt\_\-wuchty}}
+\subsubsection[{subopt}]{\setlength{\rightskip}{0pt plus 5cm}{\bf SOLUTION}$\ast$ subopt (char $\ast$ {\em seq}, \/  char $\ast$ {\em structure}, \/  int {\em delta}, \/  FILE $\ast$ {\em fp})}}
+\label{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}
 
-Returns list of subopt structures or writes to fp. 
 
-This function produces {\bfseries all} suboptimal secondary structures within 'delta' $\ast$ 0.\-01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not N\-U\-L\-L), or (fp==N\-U\-L\-L) returned in a \hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ list terminated by an entry were the 'structure' pointer is N\-U\-L\-L.
+Returns list of subopt structures or writes to fp. This function produces {\bfseries all} suboptimal secondary structures within 'delta' $\ast$ 0.01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a \hyperlink{structSOLUTION}{SOLUTION} $\ast$ list terminated by an entry were the 'structure' pointer is NULL.
 
 
 \begin{DoxyParams}{Parameters}
-{\em seq} & \\
-\hline
-{\em structure} & \\
-\hline
-{\em delta} & \\
-\hline
-{\em fp} & \\
-\hline
-\end{DoxyParams}
+\item[{\em seq}]\item[{\em structure}]\item[{\em delta}]\item[{\em fp}]\end{DoxyParams}
 \begin{DoxyReturn}{Returns}
 
 \end{DoxyReturn}
-\hypertarget{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{\index{Suboptimal structures within an energy band arround the M\-F\-E@{Suboptimal structures within an energy band arround the M\-F\-E}!subopt\-\_\-circ@{subopt\-\_\-circ}}
-\index{subopt\-\_\-circ@{subopt\-\_\-circ}!Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the M\-F\-E}}
-\subsubsection[{subopt\-\_\-circ}]{\setlength{\rightskip}{0pt plus 5cm}{\bf S\-O\-L\-U\-T\-I\-O\-N}$\ast$ subopt\-\_\-circ (
-\begin{DoxyParamCaption}
-\item[{char $\ast$}]{seq, }
-\item[{char $\ast$}]{sequence, }
-\item[{int}]{delta, }
-\item[{F\-I\-L\-E $\ast$}]{fp}
-\end{DoxyParamCaption}
-)}}\label{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}
-
+\hypertarget{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{
+\index{subopt\_\-wuchty@{subopt\_\-wuchty}!subopt\_\-circ@{subopt\_\-circ}}
+\index{subopt\_\-circ@{subopt\_\-circ}!subopt_wuchty@{subopt\_\-wuchty}}
+\subsubsection[{subopt\_\-circ}]{\setlength{\rightskip}{0pt plus 5cm}{\bf SOLUTION}$\ast$ subopt\_\-circ (char $\ast$ {\em seq}, \/  char $\ast$ {\em sequence}, \/  int {\em delta}, \/  FILE $\ast$ {\em fp})}}
+\label{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}
 
-Returns list of circular subopt structures or writes to fp. 
 
-This function is similar to \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()} but calculates secondary structures assuming the R\-N\-A sequence to be circular instead of linear
+Returns list of circular subopt structures or writes to fp. This function is similar to \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()} but calculates secondary structures assuming the RNA sequence to be circular instead of linear
 
 
 \begin{DoxyParams}{Parameters}
-{\em seq} & \\
-\hline
-{\em sequence} & \\
-\hline
-{\em delta} & \\
-\hline
-{\em fp} & \\
-\hline
-\end{DoxyParams}
+\item[{\em seq}]\item[{\em sequence}]\item[{\em delta}]\item[{\em fp}]\end{DoxyParams}
 \begin{DoxyReturn}{Returns}
 
 \end{DoxyReturn}