-\hypertarget{group__mfe__cofold}{\section{M\-F\-E Structures of two hybridized Sequences}
-\label{group__mfe__cofold}\index{M\-F\-E Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}}
+\hypertarget{group__mfe__cofold}{
+\section{MFE Structures of two hybridized Sequences}
+\label{group__mfe__cofold}\index{MFE Structures of two hybridized Sequences@{MFE Structures of two hybridized Sequences}}
}
-Collaboration diagram for M\-F\-E Structures of two hybridized Sequences\-:
-\nopagebreak
+
+
+Collaboration diagram for MFE Structures of two hybridized Sequences:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__mfe__cofold}
+\includegraphics[width=300pt]{group__mfe__cofold}
\end{center}
\end{figure}
\subsection*{Files}
\begin{DoxyCompactItemize}
\item
-file \hyperlink{cofold_8h}{cofold.\-h}
-\begin{DoxyCompactList}\small\item\em M\-F\-E version of cofolding routines. \end{DoxyCompactList}\end{DoxyCompactItemize}
+file \hyperlink{cofold_8h}{cofold.h}
+
+
+\begin{DoxyCompactList}\small\item\em MFE version of cofolding routines. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item
float \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold} (const char $\ast$sequence, char $\ast$structure)
-\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting R\-N\-A molecules. \end{DoxyCompactList}\item
-\hypertarget{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{float \hyperlink{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{cofold\-\_\-par} (const char $\ast$string, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int is\-\_\-constrained)}\label{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}
-
-\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting R\-N\-A molecules. \end{DoxyCompactList}\item
-\hypertarget{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{void \hyperlink{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{free\-\_\-co\-\_\-arrays} (void)}\label{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}
+\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting RNA molecules. \item\end{DoxyCompactList}\item
+\hypertarget{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{
+float \hyperlink{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{cofold\_\-par} (const char $\ast$string, char $\ast$structure, \hyperlink{structparamT}{paramT} $\ast$parameters, int is\_\-constrained)}
+\label{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}
-\begin{DoxyCompactList}\small\item\em Free memory occupied by \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold()} \end{DoxyCompactList}\item
-\hypertarget{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{void \hyperlink{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{update\-\_\-cofold\-\_\-params} (void)}\label{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}
+\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting RNA molecules. \item\end{DoxyCompactList}\item
+\hypertarget{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{
+void \hyperlink{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{free\_\-co\_\-arrays} (void)}
+\label{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}
-\begin{DoxyCompactList}\small\item\em Recalculate parameters. \end{DoxyCompactList}\item
-void \hyperlink{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{export\-\_\-cofold\-\_\-arrays\-\_\-gq} (int $\ast$$\ast$f5\-\_\-p, int $\ast$$\ast$c\-\_\-p, int $\ast$$\ast$f\-M\-L\-\_\-p, int $\ast$$\ast$f\-M1\-\_\-p, int $\ast$$\ast$fc\-\_\-p, int $\ast$$\ast$ggg\-\_\-p, int $\ast$$\ast$indx\-\_\-p, char $\ast$$\ast$ptype\-\_\-p)
-\begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold (with gquadruplex support) \end{DoxyCompactList}\item
-void \hyperlink{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{export\-\_\-cofold\-\_\-arrays} (int $\ast$$\ast$f5\-\_\-p, int $\ast$$\ast$c\-\_\-p, int $\ast$$\ast$f\-M\-L\-\_\-p, int $\ast$$\ast$f\-M1\-\_\-p, int $\ast$$\ast$fc\-\_\-p, int $\ast$$\ast$indx\-\_\-p, char $\ast$$\ast$ptype\-\_\-p)
-\begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\begin{DoxyCompactList}\small\item\em Free memory occupied by \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold()}. \item\end{DoxyCompactList}\item
+\hypertarget{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{
+void \hyperlink{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{update\_\-cofold\_\-params} (void)}
+\label{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}
-
-\subsection{Detailed Description}
+\begin{DoxyCompactList}\small\item\em Recalculate parameters. \item\end{DoxyCompactList}\item
+void \hyperlink{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{export\_\-cofold\_\-arrays\_\-gq} (int $\ast$$\ast$f5\_\-p, int $\ast$$\ast$c\_\-p, int $\ast$$\ast$fML\_\-p, int $\ast$$\ast$fM1\_\-p, int $\ast$$\ast$fc\_\-p, int $\ast$$\ast$ggg\_\-p, int $\ast$$\ast$indx\_\-p, char $\ast$$\ast$ptype\_\-p)
+\begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold (with gquadruplex support). \item\end{DoxyCompactList}\item
+void \hyperlink{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{export\_\-cofold\_\-arrays} (int $\ast$$\ast$f5\_\-p, int $\ast$$\ast$c\_\-p, int $\ast$$\ast$fML\_\-p, int $\ast$$\ast$fM1\_\-p, int $\ast$$\ast$fc\_\-p, int $\ast$$\ast$indx\_\-p, char $\ast$$\ast$ptype\_\-p)
+\begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection{Function Documentation}
-\hypertarget{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{\index{M\-F\-E Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}!cofold@{cofold}}
-\index{cofold@{cofold}!MFE Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}}
-\subsubsection[{cofold}]{\setlength{\rightskip}{0pt plus 5cm}float cofold (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{sequence, }
-\item[{char $\ast$}]{structure}
-\end{DoxyParamCaption}
-)}}\label{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}
-
+\hypertarget{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{
+\index{mfe\_\-cofold@{mfe\_\-cofold}!cofold@{cofold}}
+\index{cofold@{cofold}!mfe_cofold@{mfe\_\-cofold}}
+\subsubsection[{cofold}]{\setlength{\rightskip}{0pt plus 5cm}float cofold (const char $\ast$ {\em sequence}, \/ char $\ast$ {\em structure})}}
+\label{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}
-Compute the minimum free energy of two interacting R\-N\-A molecules.
-The code is analog to the \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} function. If \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point} ==-\/1 results should be the same as with \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}.
+Compute the minimum free energy of two interacting RNA molecules. The code is analog to the \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} function. If \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\_\-point} ==-\/1 results should be the same as with \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}.
\begin{DoxyParams}{Parameters}
-{\em sequence} & The two sequences concatenated \\
-\hline
-{\em structure} & Will hold the barcket dot structure of the dimer molecule \\
-\hline
-\end{DoxyParams}
+\item[{\em sequence}]The two sequences concatenated \item[{\em structure}]Will hold the barcket dot structure of the dimer molecule \end{DoxyParams}
\begin{DoxyReturn}{Returns}
minimum free energy of the structure
\end{DoxyReturn}
-\hypertarget{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{\index{M\-F\-E Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}!export\-\_\-cofold\-\_\-arrays\-\_\-gq@{export\-\_\-cofold\-\_\-arrays\-\_\-gq}}
-\index{export\-\_\-cofold\-\_\-arrays\-\_\-gq@{export\-\_\-cofold\-\_\-arrays\-\_\-gq}!MFE Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}}
-\subsubsection[{export\-\_\-cofold\-\_\-arrays\-\_\-gq}]{\setlength{\rightskip}{0pt plus 5cm}void export\-\_\-cofold\-\_\-arrays\-\_\-gq (
-\begin{DoxyParamCaption}
-\item[{int $\ast$$\ast$}]{f5\-\_\-p, }
-\item[{int $\ast$$\ast$}]{c\-\_\-p, }
-\item[{int $\ast$$\ast$}]{f\-M\-L\-\_\-p, }
-\item[{int $\ast$$\ast$}]{f\-M1\-\_\-p, }
-\item[{int $\ast$$\ast$}]{fc\-\_\-p, }
-\item[{int $\ast$$\ast$}]{ggg\-\_\-p, }
-\item[{int $\ast$$\ast$}]{indx\-\_\-p, }
-\item[{char $\ast$$\ast$}]{ptype\-\_\-p}
-\end{DoxyParamCaption}
-)}}\label{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}
-
+\hypertarget{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{
+\index{mfe\_\-cofold@{mfe\_\-cofold}!export\_\-cofold\_\-arrays\_\-gq@{export\_\-cofold\_\-arrays\_\-gq}}
+\index{export\_\-cofold\_\-arrays\_\-gq@{export\_\-cofold\_\-arrays\_\-gq}!mfe_cofold@{mfe\_\-cofold}}
+\subsubsection[{export\_\-cofold\_\-arrays\_\-gq}]{\setlength{\rightskip}{0pt plus 5cm}void export\_\-cofold\_\-arrays\_\-gq (int $\ast$$\ast$ {\em f5\_\-p}, \/ int $\ast$$\ast$ {\em c\_\-p}, \/ int $\ast$$\ast$ {\em fML\_\-p}, \/ int $\ast$$\ast$ {\em fM1\_\-p}, \/ int $\ast$$\ast$ {\em fc\_\-p}, \/ int $\ast$$\ast$ {\em ggg\_\-p}, \/ int $\ast$$\ast$ {\em indx\_\-p}, \/ char $\ast$$\ast$ {\em ptype\_\-p})}}
+\label{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}
-Export the arrays of partition function cofold (with gquadruplex support)
-Export the cofold arrays for use e.\-g. in the concentration Computations or suboptimal secondary structure backtracking
+Export the arrays of partition function cofold (with gquadruplex support). Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking
\begin{DoxyParams}{Parameters}
-{\em f5\-\_\-p} & A pointer to the 'f5' array, i.\-e. array conatining best free energy in interval \mbox{[}1,j\mbox{]} \\
-\hline
-{\em c\-\_\-p} & A pointer to the 'c' array, i.\-e. array containing best free energy in interval \mbox{[}i,j\mbox{]} given that i pairs with j \\
-\hline
-{\em f\-M\-L\-\_\-p} & A pointer to the 'M' array, i.\-e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for any multiloop segment with at least one stem \\
-\hline
-{\em f\-M1\-\_\-p} & A pointer to the 'M1' array, i.\-e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for multiloop segment with exactly one stem \\
-\hline
-{\em fc\-\_\-p} & A pointer to the 'fc' array, i.\-e. array ... \\
-\hline
-{\em ggg\-\_\-p} & A pointer to the 'ggg' array, i.\-e. array containing best free energy of a gquadruplex delimited by \mbox{[}i,j\mbox{]} \\
-\hline
-{\em indx\-\_\-p} & A pointer to the indexing array used for accessing the energy matrices \\
-\hline
-{\em ptype\-\_\-p} & A pointer to the ptype array containing the base pair types for each possibility (i,j) \\
-\hline
-\end{DoxyParams}
-\hypertarget{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{\index{M\-F\-E Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}!export\-\_\-cofold\-\_\-arrays@{export\-\_\-cofold\-\_\-arrays}}
-\index{export\-\_\-cofold\-\_\-arrays@{export\-\_\-cofold\-\_\-arrays}!MFE Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}}
-\subsubsection[{export\-\_\-cofold\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void export\-\_\-cofold\-\_\-arrays (
-\begin{DoxyParamCaption}
-\item[{int $\ast$$\ast$}]{f5\-\_\-p, }
-\item[{int $\ast$$\ast$}]{c\-\_\-p, }
-\item[{int $\ast$$\ast$}]{f\-M\-L\-\_\-p, }
-\item[{int $\ast$$\ast$}]{f\-M1\-\_\-p, }
-\item[{int $\ast$$\ast$}]{fc\-\_\-p, }
-\item[{int $\ast$$\ast$}]{indx\-\_\-p, }
-\item[{char $\ast$$\ast$}]{ptype\-\_\-p}
-\end{DoxyParamCaption}
-)}}\label{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}
-
-
-Export the arrays of partition function cofold.
-
-Export the cofold arrays for use e.\-g. in the concentration Computations or suboptimal secondary structure backtracking
+\item[{\em f5\_\-p}]A pointer to the 'f5' array, i.e. array conatining best free energy in interval \mbox{[}1,j\mbox{]} \item[{\em c\_\-p}]A pointer to the 'c' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} given that i pairs with j \item[{\em fML\_\-p}]A pointer to the 'M' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for any multiloop segment with at least one stem \item[{\em fM1\_\-p}]A pointer to the 'M1' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for multiloop segment with exactly one stem \item[{\em fc\_\-p}]A pointer to the 'fc' array, i.e. array ... \item[{\em ggg\_\-p}]A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by \mbox{[}i,j\mbox{]} \item[{\em indx\_\-p}]A pointer to the indexing array used for accessing the energy matrices \item[{\em ptype\_\-p}]A pointer to the ptype array containing the base pair types for each possibility (i,j) \end{DoxyParams}
+\hypertarget{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{
+\index{mfe\_\-cofold@{mfe\_\-cofold}!export\_\-cofold\_\-arrays@{export\_\-cofold\_\-arrays}}
+\index{export\_\-cofold\_\-arrays@{export\_\-cofold\_\-arrays}!mfe_cofold@{mfe\_\-cofold}}
+\subsubsection[{export\_\-cofold\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void export\_\-cofold\_\-arrays (int $\ast$$\ast$ {\em f5\_\-p}, \/ int $\ast$$\ast$ {\em c\_\-p}, \/ int $\ast$$\ast$ {\em fML\_\-p}, \/ int $\ast$$\ast$ {\em fM1\_\-p}, \/ int $\ast$$\ast$ {\em fc\_\-p}, \/ int $\ast$$\ast$ {\em indx\_\-p}, \/ char $\ast$$\ast$ {\em ptype\_\-p})}}
+\label{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}
+
+
+Export the arrays of partition function cofold. Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking
\begin{DoxyParams}{Parameters}
-{\em f5\-\_\-p} & A pointer to the 'f5' array, i.\-e. array conatining best free energy in interval \mbox{[}1,j\mbox{]} \\
-\hline
-{\em c\-\_\-p} & A pointer to the 'c' array, i.\-e. array containing best free energy in interval \mbox{[}i,j\mbox{]} given that i pairs with j \\
-\hline
-{\em f\-M\-L\-\_\-p} & A pointer to the 'M' array, i.\-e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for any multiloop segment with at least one stem \\
-\hline
-{\em f\-M1\-\_\-p} & A pointer to the 'M1' array, i.\-e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for multiloop segment with exactly one stem \\
-\hline
-{\em fc\-\_\-p} & A pointer to the 'fc' array, i.\-e. array ... \\
-\hline
-{\em indx\-\_\-p} & A pointer to the indexing array used for accessing the energy matrices \\
-\hline
-{\em ptype\-\_\-p} & A pointer to the ptype array containing the base pair types for each possibility (i,j) \\
-\hline
-\end{DoxyParams}
+\item[{\em f5\_\-p}]A pointer to the 'f5' array, i.e. array conatining best free energy in interval \mbox{[}1,j\mbox{]} \item[{\em c\_\-p}]A pointer to the 'c' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} given that i pairs with j \item[{\em fML\_\-p}]A pointer to the 'M' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for any multiloop segment with at least one stem \item[{\em fM1\_\-p}]A pointer to the 'M1' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for multiloop segment with exactly one stem \item[{\em fc\_\-p}]A pointer to the 'fc' array, i.e. array ... \item[{\em indx\_\-p}]A pointer to the indexing array used for accessing the energy matrices \item[{\em ptype\_\-p}]A pointer to the ptype array containing the base pair types for each possibility (i,j) \end{DoxyParams}
git://source.jalview.org / jabaws.git / blobdiff