-\hypertarget{group__kl__neighborhood__stochbt}{\section{Stochastic Backtracking of Structures from Distance Based Partitioning}
+\hypertarget{group__kl__neighborhood__stochbt}{
+\section{Stochastic Backtracking of Structures from Distance Based Partitioning}
\label{group__kl__neighborhood__stochbt}\index{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
}
Contains functions related to stochastic backtracking from a specified distance class.
-Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning\-:
-\nopagebreak
+Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__kl__neighborhood__stochbt}
+\includegraphics[width=354pt]{group__kl__neighborhood__stochbt}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item
-char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int d1, int d2)
-\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. \end{DoxyCompactList}\item
-char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{Two\-Dpfold\-\_\-pbacktrack5} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int d1, int d2, unsigned int length)
-\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. \end{DoxyCompactList}\end{DoxyCompactItemize}
+char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold\_\-pbacktrack} (\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$vars, int d1, int d2)
+\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. \item\end{DoxyCompactList}\item
+char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{TwoDpfold\_\-pbacktrack5} (\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$vars, int d1, int d2, unsigned int length)
+\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection{Detailed Description}
Contains functions related to stochastic backtracking from a specified distance class.
\subsection{Function Documentation}
-\hypertarget{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{\index{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}!Two\-Dpfold\-\_\-pbacktrack@{Two\-Dpfold\-\_\-pbacktrack}}
-\index{Two\-Dpfold\-\_\-pbacktrack@{Two\-Dpfold\-\_\-pbacktrack}!Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
-\subsubsection[{Two\-Dpfold\-\_\-pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Two\-Dpfold\-\_\-pbacktrack (
-\begin{DoxyParamCaption}
-\item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars, }
-\item[{int}]{d1, }
-\item[{int}]{d2}
-\end{DoxyParamCaption}
-)}}\label{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}
+\hypertarget{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{
+\index{kl\_\-neighborhood\_\-stochbt@{kl\_\-neighborhood\_\-stochbt}!TwoDpfold\_\-pbacktrack@{TwoDpfold\_\-pbacktrack}}
+\index{TwoDpfold\_\-pbacktrack@{TwoDpfold\_\-pbacktrack}!kl_neighborhood_stochbt@{kl\_\-neighborhood\_\-stochbt}}
+\subsubsection[{TwoDpfold\_\-pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ TwoDpfold\_\-pbacktrack ({\bf TwoDpfold\_\-vars} $\ast$ {\em vars}, \/ int {\em d1}, \/ int {\em d2})}}
+\label{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}
-Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability.
-
-If the argument 'd1' is set to '-\/1', the structure will be backtracked in the distance class where all structures exceeding the maximum basepair distance to either of the references reside.
+Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. If the argument 'd1' is set to '-\/1', the structure will be backtracked in the distance class where all structures exceeding the maximum basepair distance to either of the references reside.
\begin{DoxyPrecond}{Precondition}
-The argument 'vars' must contain precalculated partition function matrices, i.\-e. a call to \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()} preceding this function is mandatory!
+The argument 'vars' must contain precalculated partition function matrices, i.e. a call to \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()} preceding this function is mandatory!
\end{DoxyPrecond}
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()}
\end{DoxySeeAlso}
-\begin{DoxyParams}[1]{Parameters}
-\mbox{\tt in} & {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
-\hline
-\mbox{\tt in} & {\em d1} & the distance to reference1 (may be -\/1) \\
-\hline
-\mbox{\tt in} & {\em d2} & the distance to reference2 \\
-\hline
-\end{DoxyParams}
+\begin{DoxyParams}{Parameters}
+\item[\mbox{$\leftarrow$} {\em vars}]the datastructure containing all necessary folding attributes and matrices \item[\mbox{$\leftarrow$} {\em d1}]the distance to reference1 (may be -\/1) \item[\mbox{$\leftarrow$} {\em d2}]the distance to reference2 \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A sampled secondary structure in dot-\/bracket notation
\end{DoxyReturn}
-\hypertarget{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{\index{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}!Two\-Dpfold\-\_\-pbacktrack5@{Two\-Dpfold\-\_\-pbacktrack5}}
-\index{Two\-Dpfold\-\_\-pbacktrack5@{Two\-Dpfold\-\_\-pbacktrack5}!Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
-\subsubsection[{Two\-Dpfold\-\_\-pbacktrack5}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Two\-Dpfold\-\_\-pbacktrack5 (
-\begin{DoxyParamCaption}
-\item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars, }
-\item[{int}]{d1, }
-\item[{int}]{d2, }
-\item[{unsigned int}]{length}
-\end{DoxyParamCaption}
-)}}\label{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}
-
+\hypertarget{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{
+\index{kl\_\-neighborhood\_\-stochbt@{kl\_\-neighborhood\_\-stochbt}!TwoDpfold\_\-pbacktrack5@{TwoDpfold\_\-pbacktrack5}}
+\index{TwoDpfold\_\-pbacktrack5@{TwoDpfold\_\-pbacktrack5}!kl_neighborhood_stochbt@{kl\_\-neighborhood\_\-stochbt}}
+\subsubsection[{TwoDpfold\_\-pbacktrack5}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ TwoDpfold\_\-pbacktrack5 ({\bf TwoDpfold\_\-vars} $\ast$ {\em vars}, \/ int {\em d1}, \/ int {\em d2}, \/ unsigned int {\em length})}}
+\label{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}
-Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability.
-This function does essentially the same as Two\-Dpfold\-\_\-pbacktrack with the only difference that partial structures, i.\-e. structures beginning from the 5' end with a specified length of the sequence, are backtracked
+Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. This function does essentially the same as TwoDpfold\_\-pbacktrack with the only difference that partial structures, i.e. structures beginning from the 5' end with a specified length of the sequence, are backtracked
\begin{DoxyNote}{Note}
-This function does not work (since it makes no sense) for circular R\-N\-A sequences!
+This function does not work (since it makes no sense) for circular RNA sequences!
\end{DoxyNote}
\begin{DoxyPrecond}{Precondition}
-The argument 'vars' must contain precalculated partition function matrices, i.\-e. a call to \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()} preceding this function is mandatory!
+The argument 'vars' must contain precalculated partition function matrices, i.e. a call to \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()} preceding this function is mandatory!
\end{DoxyPrecond}
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold\_\-pbacktrack()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()}
\end{DoxySeeAlso}
-\begin{DoxyParams}[1]{Parameters}
-\mbox{\tt in} & {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
-\hline
-\mbox{\tt in} & {\em d1} & the distance to reference1 (may be -\/1) \\
-\hline
-\mbox{\tt in} & {\em d2} & the distance to reference2 \\
-\hline
-\mbox{\tt in} & {\em length} & the length of the structure beginning from the 5' end \\
-\hline
-\end{DoxyParams}
+\begin{DoxyParams}{Parameters}
+\item[\mbox{$\leftarrow$} {\em vars}]the datastructure containing all necessary folding attributes and matrices \item[\mbox{$\leftarrow$} {\em d1}]the distance to reference1 (may be -\/1) \item[\mbox{$\leftarrow$} {\em d2}]the distance to reference2 \item[\mbox{$\leftarrow$} {\em length}]the length of the structure beginning from the 5' end \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A sampled secondary structure in dot-\/bracket notation
\end{DoxyReturn}
git://source.jalview.org / jabaws.git / blobdiff