-\hypertarget{group__consensus__pf__fold}{\section{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
+\hypertarget{group__consensus__pf__fold}{
+\section{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
\label{group__consensus__pf__fold}\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
}
-Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s)\-:
-\nopagebreak
+
+
+Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s):\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__consensus__pf__fold}
+\includegraphics[width=334pt]{group__consensus__pf__fold}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item
-float \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\-\_\-fold\-\_\-par} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained, int is\-\_\-circular)
+float \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\_\-fold\_\-par} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl, \hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$parameters, int calculate\_\-bppm, int is\_\-constrained, int is\_\-circular)
\item
-float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
-\begin{DoxyCompactList}\small\item\em The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\-\_\-info} structs. The list is terminated by the first entry with pi.\-i = 0. \end{DoxyCompactList}\item
-float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
+float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
+\begin{DoxyCompactList}\small\item\em The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\_\-info} structs. The list is terminated by the first entry with pi.i = 0. \item\end{DoxyCompactList}\item
+float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\_\-circ\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
\item
-double $\ast$ \hyperlink{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{export\-\_\-ali\-\_\-bppm} (void)
-\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\end{DoxyCompactItemize}
-
-
-\subsection{Detailed Description}
+FLT\_\-OR\_\-DBL $\ast$ \hyperlink{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{export\_\-ali\_\-bppm} (void)
+\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection{Function Documentation}
-\hypertarget{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-fold\-\_\-par@{alipf\-\_\-fold\-\_\-par}}
-\index{alipf\-\_\-fold\-\_\-par@{alipf\-\_\-fold\-\_\-par}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
-\subsubsection[{alipf\-\_\-fold\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-fold\-\_\-par (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$$\ast$}]{sequences, }
-\item[{char $\ast$}]{structure, }
-\item[{{\bf plist} $\ast$$\ast$}]{pl, }
-\item[{{\bf pf\-\_\-param\-T} $\ast$}]{parameters, }
-\item[{int}]{calculate\-\_\-bppm, }
-\item[{int}]{is\-\_\-constrained, }
-\item[{int}]{is\-\_\-circular}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}
+\hypertarget{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{
+\index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-fold\_\-par@{alipf\_\-fold\_\-par}}
+\index{alipf\_\-fold\_\-par@{alipf\_\-fold\_\-par}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
+\subsubsection[{alipf\_\-fold\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-fold\_\-par (const char $\ast$$\ast$ {\em sequences}, \/ char $\ast$ {\em structure}, \/ {\bf plist} $\ast$$\ast$ {\em pl}, \/ {\bf pf\_\-paramT} $\ast$ {\em parameters}, \/ int {\em calculate\_\-bppm}, \/ int {\em is\_\-constrained}, \/ int {\em is\_\-circular})}}
+\label{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}
\begin{DoxyParams}{Parameters}
-{\em sequences} & \\
-\hline
-{\em structure} & \\
-\hline
-{\em pl} & \\
-\hline
-{\em parameters} & \\
-\hline
-{\em calculate\-\_\-bppm} & \\
-\hline
-{\em is\-\_\-constrained} & \\
-\hline
-{\em is\-\_\-circular} & \\
-\hline
-\end{DoxyParams}
+\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\item[{\em parameters}]\item[{\em calculate\_\-bppm}]\item[{\em is\_\-constrained}]\item[{\em is\_\-circular}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}
\end{DoxyReturn}
-\hypertarget{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-fold@{alipf\-\_\-fold}}
-\index{alipf\-\_\-fold@{alipf\-\_\-fold}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
-\subsubsection[{alipf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-fold (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$$\ast$}]{sequences, }
-\item[{char $\ast$}]{structure, }
-\item[{{\bf plist} $\ast$$\ast$}]{pl}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}
-
-
-The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\-\_\-info} structs. The list is terminated by the first entry with pi.\-i = 0.
+\hypertarget{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{
+\index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-fold@{alipf\_\-fold}}
+\index{alipf\_\-fold@{alipf\_\-fold}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
+\subsubsection[{alipf\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-fold (const char $\ast$$\ast$ {\em sequences}, \/ char $\ast$ {\em structure}, \/ {\bf plist} $\ast$$\ast$ {\em pl})}}
+\label{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}
+The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\_\-info} structs. The list is terminated by the first entry with pi.i = 0.
\begin{DoxyParams}{Parameters}
-{\em sequences} & \\
-\hline
-{\em structure} & \\
-\hline
-{\em pl} & \\
-\hline
-\end{DoxyParams}
+\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}
\end{DoxyReturn}
-\hypertarget{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-circ\-\_\-fold@{alipf\-\_\-circ\-\_\-fold}}
-\index{alipf\-\_\-circ\-\_\-fold@{alipf\-\_\-circ\-\_\-fold}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
-\subsubsection[{alipf\-\_\-circ\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-circ\-\_\-fold (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$$\ast$}]{sequences, }
-\item[{char $\ast$}]{structure, }
-\item[{{\bf plist} $\ast$$\ast$}]{pl}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}
+\hypertarget{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{
+\index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-circ\_\-fold@{alipf\_\-circ\_\-fold}}
+\index{alipf\_\-circ\_\-fold@{alipf\_\-circ\_\-fold}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
+\subsubsection[{alipf\_\-circ\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-circ\_\-fold (const char $\ast$$\ast$ {\em sequences}, \/ char $\ast$ {\em structure}, \/ {\bf plist} $\ast$$\ast$ {\em pl})}}
+\label{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}
\begin{DoxyParams}{Parameters}
-{\em sequences} & \\
-\hline
-{\em structure} & \\
-\hline
-{\em pl} & \\
-\hline
-\end{DoxyParams}
+\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}
\end{DoxyReturn}
-\hypertarget{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!export\-\_\-ali\-\_\-bppm@{export\-\_\-ali\-\_\-bppm}}
-\index{export\-\_\-ali\-\_\-bppm@{export\-\_\-ali\-\_\-bppm}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
-\subsubsection[{export\-\_\-ali\-\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ export\-\_\-ali\-\_\-bppm (
-\begin{DoxyParamCaption}
-\item[{void}]{}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}
-
+\hypertarget{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{
+\index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!export\_\-ali\_\-bppm@{export\_\-ali\_\-bppm}}
+\index{export\_\-ali\_\-bppm@{export\_\-ali\_\-bppm}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
+\subsubsection[{export\_\-ali\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}FLT\_\-OR\_\-DBL$\ast$ export\_\-ali\_\-bppm (void)}}
+\label{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}
-Get a pointer to the base pair probability array.
-Accessing the base pair probabilities for a pair (i,j) is achieved by \begin{DoxyVerb}FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \end{DoxyVerb}
+Get a pointer to the base pair probability array. Accessing the base pair probabilities for a pair (i,j) is achieved by \begin{DoxyVerb}FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \end{DoxyVerb}
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_\-iindx()}
\end{DoxySeeAlso}
\begin{DoxyReturn}{Returns}
A pointer to the base pair probability array
git://source.jalview.org / jabaws.git / blobdiff