1 \hypertarget{group__consensus__pf__fold}{\section{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
2 \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)}}
4 Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s)\-:
9 \includegraphics[width=350pt]{group__consensus__pf__fold}
12 \subsection*{Functions}
13 \begin{DoxyCompactItemize}
15 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)
17 float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
18 \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
19 float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
21 double $\ast$ \hyperlink{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{export\-\_\-ali\-\_\-bppm} (void)
22 \begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\end{DoxyCompactItemize}
25 \subsection{Detailed Description}
28 \subsection{Function Documentation}
29 \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}}
30 \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)}}
31 \subsubsection[{alipf\-\_\-fold\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-fold\-\_\-par (
32 \begin{DoxyParamCaption}
33 \item[{const char $\ast$$\ast$}]{sequences, }
34 \item[{char $\ast$}]{structure, }
35 \item[{{\bf plist} $\ast$$\ast$}]{pl, }
36 \item[{{\bf pf\-\_\-param\-T} $\ast$}]{parameters, }
37 \item[{int}]{calculate\-\_\-bppm, }
38 \item[{int}]{is\-\_\-constrained, }
39 \item[{int}]{is\-\_\-circular}
40 \end{DoxyParamCaption}
41 )}}\label{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}
43 \begin{DoxyParams}{Parameters}
52 {\em calculate\-\_\-bppm} & \\
54 {\em is\-\_\-constrained} & \\
56 {\em is\-\_\-circular} & \\
59 \begin{DoxyReturn}{Returns}
62 \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}}
63 \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)}}
64 \subsubsection[{alipf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-fold (
65 \begin{DoxyParamCaption}
66 \item[{const char $\ast$$\ast$}]{sequences, }
67 \item[{char $\ast$}]{structure, }
68 \item[{{\bf plist} $\ast$$\ast$}]{pl}
69 \end{DoxyParamCaption}
70 )}}\label{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}
73 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.
76 \begin{DoxyParams}{Parameters}
84 \begin{DoxyReturn}{Returns}
87 \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}}
88 \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)}}
89 \subsubsection[{alipf\-\_\-circ\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-circ\-\_\-fold (
90 \begin{DoxyParamCaption}
91 \item[{const char $\ast$$\ast$}]{sequences, }
92 \item[{char $\ast$}]{structure, }
93 \item[{{\bf plist} $\ast$$\ast$}]{pl}
94 \end{DoxyParamCaption}
95 )}}\label{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}
97 \begin{DoxyParams}{Parameters}
105 \begin{DoxyReturn}{Returns}
108 \hypertarget{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!export\-\_\-ali\-\_\-bppm@{export\-\_\-ali\-\_\-bppm}}
109 \index{export\-\_\-ali\-\_\-bppm@{export\-\_\-ali\-\_\-bppm}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
110 \subsubsection[{export\-\_\-ali\-\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ export\-\_\-ali\-\_\-bppm (
111 \begin{DoxyParamCaption}
113 \end{DoxyParamCaption}
114 )}}\label{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}
117 Get a pointer to the base pair probability array.
119 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}
122 \begin{DoxySeeAlso}{See Also}
123 \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()}
125 \begin{DoxyReturn}{Returns}
126 A pointer to the base pair probability array